Build log for relion (3.1.3-3) on armhf

relion → 3.1.3-3 → armhf → 2022-12-11 10:01:01

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02

+==============================================================================+
| relion 3.1.3-3 (armhf)                       Sun, 11 Dec 2022 07:36:39 +0000 |
+==============================================================================+

Package: relion
Version: 3.1.3-3
Source Version: 3.1.3-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-3aeb9ac9-415a-4bc2-9780-f6790fbf8b1e' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.8 MB in 29s (963 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'relion' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/relion.git
Please use:
git clone https://salsa.debian.org/med-team/relion.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2360 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main relion 3.1.3-3 (dsc) [2136 B]
Get:2 http://172.17.4.1/private bookworm-staging/main relion 3.1.3-3 (tar) [2345 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main relion 3.1.3-3 (diff) [12.0 kB]
Fetched 2360 kB in 0s (8124 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/relion-tjr4JL/relion-3.1.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/relion-tjr4JL' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-Bk2v7v/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Bk2v7v/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2398 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  krb5-locales libldap-common libpam-cap libperl5.34 netbase perl-modules-5.34
  sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 84 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (16.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15027 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid
Filtered Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid
dpkg-deb: building package 'sbuild-build-depends-relion-dummy' in '/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive/sbuild-build-depends-relion-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-relion-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ Sources [525 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ Packages [609 B]
Fetched 2467 B in 1s (2345 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install relion build dependencies (apt-based resolver)
------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  krb5-locales libldap-common libpam-cap libperl5.34 netbase perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils bsdutils cmake
  cmake-data cpp-12 debhelper dh-autoreconf dh-strip-nondeterminism dwz file
  fluid fontconfig-config fonts-dejavu-core g++-12 gcc-12 gcc-12-base gettext
  gettext-base gfortran-12 groff-base ibverbs-providers intltool-debian
  libarchive-zip-perl libarchive13 libasan8 libatomic1 libblkid1 libbrotli1
  libbsd0 libcairo2 libcbor0.8 libcc1-0 libcurl4 libdebhelper-perl
  libdeflate-dev libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-nouveau2
  libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
  libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
  libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
  libfftw3-double3 libfftw3-single3 libfido2-1
  libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3
  libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1
  libfreetype6 libgcc-12-dev libgcc-s1 libgfortran-12-dev libgfortran5 libgl1
  libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1
  libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu72
  libjbig-dev libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
  libjs-jquery libjs-jquery-ui libjsoncpp25 liblerc-dev liblerc4 libllvm14
  libltdl-dev libltdl7 liblzma-dev liblzma5 libmagic-mgc libmagic1 libmd0
  libmount1 libmunge2 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev
  libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
  libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev libpmix2
  libpng16-16 libprocps8 libpsl5 libpthread-stubs0-dev librdmacm1 librhash0
  librtmp1 libsensors-config libsensors5 libsmartcols1 libssh2-1 libssl3
  libstdc++-12-dev libstdc++6 libsub-override-perl libtiff-dev libtiff5
  libtiffxx5 libtool libubsan1 libuchardet0 libuuid1 libuv1 libwebp7 libx11-6
  libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
  libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0
  libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcursor1 libxdmcp-dev
  libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxnvctrl0
  libxrender1 libxshmfence1 libxxf86vm1 libz3-4 m4 man-db mount
  ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
  procps ucf util-linux util-linux-extra x11proto-dev xorg-sgml-doctools
  xtrans-dev xz-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
  elpa-cmake-mode ninja-build gcc-12-locales cpp-12-doc dh-make gcc-12-doc
  gettext-doc libasprintf-dev libgettextpo-dev gfortran-12-doc libcoarrays-dev
  groff lrzip libfftw3-doc fltk1.3-doc libcairo2-dev libpng-dev libxext-dev
  libxft-dev libxinerama-dev libjs-jquery-ui-docs libtool-doc liblzma-doc
  cryptsetup-bin openmpi-doc pciutils lm-sensors libstdc++-12-doc gcj-jdk
  libx11-doc libxcb-doc m4-doc apparmor less www-browser nfs-common opencl-icd
  gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass
  libmail-box-perl dosfstools kbd util-linux-locales
Recommended packages:
  fltk1.3-doc curl | wget | lynx ca-certificates libarchive-cpio-perl
  libgl-dev libglu1-mesa-dev | libglu-dev javascript-common libgpm2
  libcoarrays-openmpi-dev publicsuffix uuid-runtime xauth
  libmail-sendmail-perl psmisc
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
  debhelper dh-autoreconf dh-strip-nondeterminism dwz file fluid
  fontconfig-config fonts-dejavu-core gettext gettext-base gfortran-12
  groff-base ibverbs-providers intltool-debian libarchive-zip-perl
  libarchive13 libbrotli1 libbsd0 libcairo2 libcbor0.8 libcurl4
  libdebhelper-perl libdeflate-dev libdeflate0 libdrm-amdgpu1 libdrm-common
  libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-2.1-7
  libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
  libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
  libfftw3-double3 libfftw3-single3 libfido2-1
  libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3
  libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1
  libfreetype6 libgfortran-12-dev libgfortran5 libgl1 libgl1-mesa-dri
  libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libhwloc-dev libhwloc-plugins
  libhwloc15 libibverbs-dev libibverbs1 libicu72 libjbig-dev libjbig0
  libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libjs-jquery-ui
  libjsoncpp25 liblerc-dev liblerc4 libllvm14 libltdl-dev libltdl7 liblzma-dev
  libmagic-mgc libmagic1 libmd0 libmunge2 libncurses6 libnghttp2-14
  libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev
  libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0
  libpmix-dev libpmix2 libpng16-16 libprocps8 libpsl5 libpthread-stubs0-dev
  librdmacm1 librhash0 librtmp1 libsensors-config libsensors5 libssh2-1
  libsub-override-perl libtiff-dev libtiff5 libtiffxx5 libtool libuchardet0
  libuv1 libwebp7 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev
  libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
  libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev
  libxcursor1 libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1
  libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxxf86vm1 libz3-4 m4 man-db
  ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
  procps sbuild-build-depends-relion-dummy ucf x11proto-dev xorg-sgml-doctools
  xtrans-dev zlib1g-dev
The following packages will be upgraded:
  bsdutils cpp-12 g++-12 gcc-12 gcc-12-base libasan8 libatomic1 libblkid1
  libcc1-0 libgcc-12-dev libgcc-s1 libgomp1 liblzma5 libmount1 libsmartcols1
  libssl3 libstdc++-12-dev libstdc++6 libubsan1 libuuid1 mount util-linux
  util-linux-extra xz-utils
24 upgraded, 168 newly installed, 0 to remove and 60 not upgraded.
Need to get 127 MB of archives.
After this operation, 367 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Bk2v7v/apt_archive ./ sbuild-build-depends-relion-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdutils armhf 1:2.38.1-4 [83.9 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libsmartcols1 armhf 2.38.1-4 [91.6 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf util-linux-extra armhf 2.38.1-4 [98.1 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf util-linux armhf 2.38.1-4 [1062 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf mount armhf 2.38.1-4 [126 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 12.2.0-9+rpi1 [32.2 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 12.2.0-9+rpi1 [95.4 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 12.2.0-9+rpi1 [8224 B]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libasan8 armhf 12.2.0-9+rpi1 [2089 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 12.2.0-9+rpi1 [861 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf gcc-12-base armhf 12.2.0-9+rpi1 [37.2 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 12.2.0-9+rpi1 [504 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf g++-12 armhf 12.2.0-9+rpi1 [7913 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-12-dev armhf 12.2.0-9+rpi1 [2025 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libgcc-12-dev armhf 12.2.0-9+rpi1 [725 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf gcc-12 armhf 12.2.0-9+rpi1 [14.2 MB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf cpp-12 armhf 12.2.0-9+rpi1 [7156 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 12.2.0-9+rpi1 [36.1 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libblkid1 armhf 2.38.1-4 [131 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf liblzma5 armhf 5.2.9-0.0 [178 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libmount1 armhf 2.38.1-4 [144 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libuuid1 armhf 2.38.1-4 [27.1 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-7.1 [41.9 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-7.1 [457 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20221030-2 [76.2 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libcbor0.8 armhf 0.8.0-2 [22.8 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.7-1 [1614 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libfido2-1 armhf 1.12.0-2 [67.6 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf openssh-client armhf 1:9.1p1-1 [813 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf xz-utils armhf 5.2.9-0.0 [336 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.6.0-1 [306 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.86.0-2 [322 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-4 [66.7 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.44.2-1+rpi1 [125 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.25.1-1 [2026 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.25.1-1 [3859 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.1 [80.8 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.1 [941 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.39-2 [258 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libxfixes3 armhf 1:6.0.0-2 [21.2 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libxcursor1 armhf 1:1.2.1-1 [38.0 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libxft2 armhf 2.3.6-1 [53.7 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libxinerama1 armhf 2:1.1.4-3 [17.4 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libfltk1.3 armhf 1.3.8-5+b1 [484 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libfltk-forms1.3 armhf 1.3.8-5+b1 [35.4 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libfltk-images1.3 armhf 1.3.8-5+b1 [46.7 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf fluid armhf 1.3.8-5+b1 [194 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-9+rpi1 [238 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-12-dev armhf 12.2.0-9+rpi1 [285 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf gfortran-12 armhf 12.2.0-9+rpi1 [7509 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.7.0-0.2 [55.0 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.2 [152 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libibverbs1 armhf 42.0-1 [53.7 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf ibverbs-providers armhf 42.0-1 [28.8 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.42.2-1 [461 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-6 [496 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.14-1 [48.1 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libdrm-common all 2.4.114-1+rpi1 [7276 B]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libdrm2 armhf 2.4.114-1+rpi1 [32.8 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf libdrm-amdgpu1 armhf 2.4.114-1+rpi1 [19.3 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libdrm-nouveau2 armhf 2.4.114-1+rpi1 [17.0 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libdrm-radeon1 armhf 2.4.114-1+rpi1 [20.7 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-5+b1 [166 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-5+b1 [125 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-5+b1 [102 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-5+b1 [57.6 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-5+b1 [62.5 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-5+b1 [280 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf librdmacm1 armhf 42.0-1 [60.3 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-3 [310 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-double3 armhf 3.3.10-1 [325 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-single3 armhf 3.3.10-1 [509 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-bin armhf 3.3.10-1 [40.8 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-dev armhf 3.3.10-1 [827 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libfltk-cairo1.3 armhf 1.3.8-5+b1 [29.8 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf libglvnd0 armhf 1.5.0-1 [51.5 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf libglapi-mesa armhf 22.2.0-1+rpi1 [84.6 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libx11-xcb1 armhf 2:1.8.1-2 [203 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf libxcb-glx0 armhf 1.15-1 [121 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf libxcb-present0 armhf 1.15-1 [105 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libxcb-sync1 armhf 1.15-1 [108 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf libxcb-xfixes0 armhf 1.15-1 [109 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf libxshmfence1 armhf 1.3-1 [8636 B]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.1 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libz3-4 armhf 4.8.12-3 [5798 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libllvm14 armhf 1:14.0.6-9+rpi1 [19.5 MB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf libsensors5 armhf 1:3.6.0-7.1 [31.6 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf libgl1-mesa-dri armhf 22.2.0-1+rpi1 [5593 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf libglx-mesa0 armhf 22.2.0-1+rpi1 [171 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf libglx0 armhf 1.5.0-1 [32.4 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf libgl1 armhf 1.5.0-1 [91.8 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf libfltk-gl1.3 armhf 1.3.8-5+b1 [56.2 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf x11proto-dev all 2022.1-1 [599 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf libxcb1-dev armhf 1.15-1 [175 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf libx11-dev armhf 2:1.8.1-2 [780 kB]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf libfltk1.3-dev armhf 1.3.8-5+b1 [790 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf libhwloc15 armhf 2.8.0-1 [130 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.15-1 [22.3 kB]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.15-1 [35.5 kB]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.7-5 [390 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.7-5 [161 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.8.0-1 [202 kB]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.17-2 [48.8 kB]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf libxnvctrl0 armhf 510.85.02-2 [26.6 kB]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.3 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.8.0-1 [20.4 kB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.7.0-0.2 [93.4 kB]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.7.0-0.2 [163 kB]
Get:171 http://172.17.4.1/private bookworm-staging/main armhf libibverbs-dev armhf 42.0-1 [188 kB]
Get:172 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:173 http://172.17.4.1/private bookworm-staging/main armhf libjbig-dev armhf 2.1-3.1+b2 [27.7 kB]
Get:174 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:175 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:176 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:177 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:178 http://172.17.4.1/private bookworm-staging/main armhf liblerc4 armhf 4.0.0+ds-2 [133 kB]
Get:179 http://172.17.4.1/private bookworm-staging/main armhf liblerc-dev armhf 4.0.0+ds-2 [147 kB]
Get:180 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.9-0.0 [234 kB]
Get:181 http://172.17.4.1/private bookworm-staging/main armhf libmunge2 armhf 0.5.14-6 [18.6 kB]
Get:182 http://172.17.4.1/private bookworm-staging/main armhf libpmix2 armhf 4.2.2-1 [530 kB]
Get:183 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.4-3+rpi1 [1795 kB]
Get:184 http://172.17.4.1/private bookworm-staging/main armhf openmpi-common all 4.1.4-3+rpi1 [165 kB]
Get:185 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:186 http://172.17.4.1/private bookworm-staging/main armhf libpmix-dev armhf 4.2.2-1 [845 kB]
Get:187 http://172.17.4.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.4-3+rpi1 [192 kB]
Get:188 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.4-3+rpi1 [920 kB]
Get:189 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2+b1 [237 kB]
Get:190 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.4.0-6 [278 kB]
Get:191 http://172.17.4.1/private bookworm-staging/main armhf libtiffxx5 armhf 4.4.0-6 [132 kB]
Get:192 http://172.17.4.1/private bookworm-staging/main armhf libtiff-dev armhf 4.4.0-6 [389 kB]
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Setting up libjbig0:armhf (2.1-3.1+b2) ...
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Setting up libuv1:armhf (1.44.2-1+rpi1) ...
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-5+b1) ...
Setting up libxcb-shm0:armhf (1.15-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
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Setting up libnl-route-3-200:armhf (3.7.0-0.2) ...
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Setting up dh-autoreconf (20) ...
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Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
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Setting up libgcc-12-dev:armhf (12.2.0-9+rpi1) ...
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Setting up dwz (0.14+20220924-2) ...
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Setting up groff-base (1.22.4-9) ...
Setting up procps (2:3.3.17-7.1) ...
Setting up libx11-6:armhf (2:1.8.1-2) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
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Setting up libfido2-1:armhf (1.12.0-2) ...
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Setting up libibverbs1:armhf (42.0-1) ...
Setting up libdrm-nouveau2:armhf (2.4.114-1+rpi1) ...
Setting up libxrender1:armhf (1:0.9.10-1.1) ...
Setting up libstdc++-12-dev:armhf (12.2.0-9+rpi1) ...
Setting up ibverbs-providers:armhf (42.0-1) ...
Setting up libdrm-radeon1:armhf (2.4.114-1+rpi1) ...
Setting up openssh-client (1:9.1p1-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
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Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libgfortran-12-dev:armhf (12.2.0-9+rpi1) ...
Setting up man-db (2.11.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ...
Setting up libxnvctrl0:armhf (510.85.02-2) ...
Setting up libnl-route-3-dev:armhf (3.7.0-0.2) ...
Setting up gcc-12 (12.2.0-9+rpi1) ...
Setting up libxfixes3:armhf (1:6.0.0-2) ...
Setting up libxinerama1:armhf (2:1.1.4-3) ...
Setting up libcurl4:armhf (7.86.0-2) ...
Setting up g++-12 (12.2.0-9+rpi1) ...
Setting up librdmacm1:armhf (42.0-1) ...
Setting up libglx-mesa0:armhf (22.2.0-1+rpi1) ...
Setting up libglx0:armhf (1.5.0-1) ...
Setting up libxcursor1:armhf (1:1.2.1-1) ...
Setting up debhelper (13.11.1) ...
Setting up libibverbs-dev:armhf (42.0-1) ...
Setting up libhwloc-plugins:armhf (2.8.0-1) ...
Setting up gfortran-12 (12.2.0-9+rpi1) ...
Setting up libgl1:armhf (1.5.0-1) ...
Setting up cmake (3.25.1-1) ...
Setting up libfabric1:armhf (1.11.0-3) ...
Setting up libpmix2:armhf (4.2.2-1) ...
Setting up libopenmpi3:armhf (4.1.4-3+rpi1) ...
Setting up libpmix-dev:armhf (4.2.2-1) ...
Setting up openmpi-bin (4.1.4-3+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.1.4-3+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Processing triggers for libc-bin (2.35-2+rpi1) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Setting up x11proto-dev (2022.1-1) ...
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Setting up libfltk1.3:armhf (1.3.8-5+b1) ...
Setting up libfltk-gl1.3:armhf (1.3.8-5+b1) ...
Setting up libfltk-images1.3:armhf (1.3.8-5+b1) ...
Setting up libcairo2:armhf (1.16.0-6) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up libfltk-forms1.3:armhf (1.3.8-5+b1) ...
Setting up libxcb1-dev:armhf (1.15-1) ...
Setting up libx11-dev:armhf (2:1.8.1-2) ...
Setting up libfltk-cairo1.3:armhf (1.3.8-5+b1) ...
Setting up fluid (1.3.8-5+b1) ...
Setting up libfltk1.3-dev:armhf (1.3.8-5+b1) ...
Setting up sbuild-build-depends-relion-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-9+rpi1 gcc-12_12.2.0-9+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-9+rpi1 libstdc++6_12.2.0-9+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 aptitude_0.8.13-5 aptitude-common_0.8.13-5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b2 cmake_3.25.1-1 cmake-data_3.25.1-1 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-9+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.11.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 fluid_1.3.8-5+b1 fontconfig-config_2.13.1-4.5 fonts-dejavu-core_2.37-2 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-9+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-9+rpi1 gcc-12-base_12.2.0-9+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-10 gettext-base_0.21-10 gfortran-12_12.2.0-9+rpi1 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-9 gzip_1.12-1 hostname_3.23 ibverbs-providers_42.0-1 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libarchive13_3.6.0-1 libasan8_12.2.0-9+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-9+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6+rpi1 libblkid1_2.38.1-4 libboost-iostreams1.74.0_1.74.0-17 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcairo2_1.16.0-6 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcbor0.8_0.8.0-2 libcc1-0_12.2.0-9+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libcurl4_7.86.0-2 libcwidget4_0.5.18-6 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.11.1 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdpkg-perl_1.21.9+rpi1 libdrm-amdgpu1_2.4.114-1+rpi1 libdrm-common_2.4.114-1+rpi1 libdrm-nouveau2_2.4.114-1+rpi1 libdrm-radeon1_2.4.114-1+rpi1 libdrm2_2.4.114-1+rpi1 libedit2_3.1-20221030-2 libelf1_0.187-2+rpi2 libevent-2.1-7_2.1.12-stable-5+b1 libevent-core-2.1-7_2.1.12-stable-5+b1 libevent-dev_2.1.12-stable-5+b1 libevent-extra-2.1-7_2.1.12-stable-5+b1 libevent-openssl-2.1-7_2.1.12-stable-5+b1 libevent-pthreads-2.1-7_2.1.12-stable-5+b1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfabric1_1.11.0-3 libfakeroot_1.29-1 libffi8_3.4.2-4 libfftw3-bin_3.3.10-1 libfftw3-dev_3.3.10-1 libfftw3-double3_3.3.10-1 libfftw3-single3_3.3.10-1 libfido2-1_1.12.0-2 libfile-stripnondeterminism-perl_1.13.0-2 libfltk-cairo1.3_1.3.8-5+b1 libfltk-forms1.3_1.3.8-5+b1 libfltk-gl1.3_1.3.8-5+b1 libfltk-images1.3_1.3.8-5+b1 libfltk1.3_1.3.8-5+b1 libfltk1.3-dev_1.3.8-5+b1 libfontconfig1_2.13.1-4.5 libfreetype6_2.12.1+dfsg-3 libgcc-12-dev_12.2.0-9+rpi1 libgcc-s1_12.2.0-9+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.2.0-9+rpi1 libgfortran5_12.2.0-9+rpi1 libgl1_1.5.0-1 libgl1-mesa-dri_22.2.0-1+rpi1 libglapi-mesa_22.2.0-1+rpi1 libglvnd0_1.5.0-1 libglx-mesa0_22.2.0-1+rpi1 libglx0_1.5.0-1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-9+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libhwloc-dev_2.8.0-1 libhwloc-plugins_2.8.0-1 libhwloc15_2.8.0-1 libibverbs-dev_42.0-1 libibverbs1_42.0-1 libicu72_72.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjbig-dev_2.1-3.1+b2 libjbig0_2.1-3.1+b2 libjpeg-dev_1:2.1.2-1 libjpeg62-turbo_1:2.1.2-1 libjpeg62-turbo-dev_1:2.1.2-1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjsoncpp25_1.9.5-4 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 libldap-2.4-2_2.4.59+dfsg-1+b1 libldap-2.5-0_2.5.13+dfsg-2+rpi1 libldap-common_2.5.13+dfsg-2+rpi1 liblerc-dev_4.0.0+ds-2 liblerc4_4.0.0+ds-2 libllvm14_1:14.0.6-9+rpi1 libltdl-dev_2.4.7-5 libltdl7_2.4.7-5 liblz4-1_1.9.4-1+rpi1 liblzma-dev_5.2.9-0.0 liblzma5_5.2.9-0.0 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-4 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libmunge2_0.5.14-6 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1 libnl-3-200_3.7.0-0.2 libnl-3-dev_3.7.0-0.2 libnl-route-3-200_3.7.0-0.2 libnl-route-3-dev_3.7.0-0.2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnuma-dev_2.0.15-1 libnuma1_2.0.15-1 libopenmpi-dev_4.1.4-3+rpi1 libopenmpi3_4.1.4-3+rpi1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpciaccess0_0.17-2 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpmix-dev_4.2.2-1 libpmix2_4.2.2-1 libpng16-16_1.6.39-2 libprocps8_2:3.3.17-7.1 libpsl5_0.21.0-1.2 libpthread-stubs0-dev_0.4-1 librdmacm1_42.0-1 libreadline8_8.2-1 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsensors-config_1:3.6.0-7.1 libsensors5_1:3.6.0-7.1 libsepol1_3.1-1 libsepol2_3.4-2 libsigc++-2.0-0v5_2.10.8-1 libsmartcols1_2.38.1-4 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-9+rpi1 libstdc++6_12.2.0-9+rpi1 libsub-override-perl_0.09-4 libsystemd0_251.5-1+rpi1 libtasn1-6_4.19.0-2 libtiff-dev_4.4.0-6 libtiff5_4.4.0-6 libtiffxx5_4.4.0-6 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libubsan1_12.2.0-9+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-4 libuv1_1.44.2-1+rpi1 libwebp7_1.2.2-2+b1 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 libx11-dev_2:1.8.1-2 libx11-xcb1_2:1.8.1-2 libxapian30_1.4.21-1 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb-dri2-0_1.15-1 libxcb-dri3-0_1.15-1 libxcb-glx0_1.15-1 libxcb-present0_1.15-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb-sync1_1.15-1 libxcb-xfixes0_1.15-1 libxcb1_1.15-1 libxcb1-dev_1.15-1 libxcursor1_1:1.2.1-1 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxfixes3_1:6.0.0-2 libxft2_2.3.6-1 libxinerama1_2:1.1.4-3 libxml2_2.9.14+dfsg-1.1 libxnvctrl0_510.85.02-2 libxrender1_1:0.9.10-1.1 libxshmfence1_1.3-1 libxxf86vm1_1:1.1.4-1+b2 libxxhash0_0.8.1-1 libz3-4_4.8.12-3 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-4 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 ocl-icd-libopencl1_2.3.1-1 openmpi-bin_4.1.4-3+rpi1 openmpi-common_4.1.4-3+rpi1 openssh-client_1:9.1p1-1 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 procps_2:3.3.17-7.1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-relion-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 ucf_3.0043 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 x11proto-dev_2022.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.9-0.0 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.BVIWd3fQ/trustedkeys.kbx': General error
gpgv: Signature made Tue Dec  6 11:51:10 2022 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./relion_3.1.3-3.dsc
dpkg-source: info: extracting relion in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking relion_3.1.3.orig.tar.gz
dpkg-source: info: unpacking relion_3.1.3-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch
dpkg-source: info: applying typos.patch

Check disc space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-3aeb9ac9-415a-4bc2-9780-f6790fbf8b1e
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package relion
dpkg-buildpackage: info: source version 3.1.3-3
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -rf build
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir /<<PKGBUILDDIR>>/build
cd /<<PKGBUILDDIR>>/build; \
CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON -DGUI=ON -DCUDA=OFF /<<PKGBUILDDIR>>
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


CMake Warning (dev) at /usr/share/cmake-3.25/Modules/CMakeDetermineCompilerId.cmake:93 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "CUDA" will no longer be dereferenced when the policy
  is set to NEW.  Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
  /usr/share/cmake-3.25/Modules/CMakeDetermineCCompiler.cmake:123 (CMAKE_DETERMINE_COMPILER_ID)
  CMakeLists.txt:6 (project)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- The C compiler identification is GNU 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- Detecting C compiler ABI info
CMake Warning (dev) at /usr/share/cmake-3.25/Modules/CMakeDetermineCompilerABI.cmake:29 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "CUDA" will no longer be dereferenced when the policy
  is set to NEW.  Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
  /usr/share/cmake-3.25/Modules/CMakeTestCCompiler.cmake:26 (CMAKE_DETERMINE_COMPILER_ABI)
  CMakeLists.txt:6 (project)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- BUILD TYPE set to the default type:  'Release'
-- Setting fallback CUDA_ARCH=35
-- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2
-- Setting cpu precision to double
-- Setting accelerated code precision to single
-- Using non-cuda compilation....
-- Found MPI_C: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so (found version "3.1") 
-- Found MPI_CXX: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- MPI_INCLUDE_PATH : /usr/lib/arm-linux-gnueabihf/openmpi/include;/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi
-- MPI_LIBRARIES : /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so
-- MPI_CXX_INCLUDE_PATH : /usr/lib/arm-linux-gnueabihf/openmpi/include;/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi
-- MPI_CXX_LIBRARIES : /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so
-- CMAKE_C_COMPILER : /usr/bin/gcc
-- CMAKE_CXX_COMPILER : /usr/bin/g++
-- MPI_C_COMPILER : /usr/bin/mpicc
-- MPI_CXX_COMPILER : /usr/bin/mpicxx
-- CMAKE_CXX_COMPILER_ID : GNU
-- Found X11: /usr/include   
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Found FLTK: fltk_images;fltk_forms;fltk  
-- X11 and FLTK were found
-- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/arm-linux-gnueabihf/libX11.so;/usr/lib/arm-linux-gnueabihf/libm.so
-- Found FFTW
-- FFTW_PATH: /usr/include
-- FFTW_INCLUDES: /usr/include
-- FFTW_LIBRARIES: /usr/lib/arm-linux-gnueabihf/libfftw3f.so;/usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for sincos
-- Looking for sincos - found
-- Looking for __sincos
-- Looking for __sincos - not found
-- Found TIFF: /usr/lib/arm-linux-gnueabihf/libtiff.so (found version "4.4.0")  
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") 
-- Could NOT find PNG (missing: PNG_LIBRARY PNG_PNG_INCLUDE_DIR) 
BUILD_SHARED_LIBS = OFF
-- Building static libs (larger build size and binaries)
Running apps/CMakeLists.txt...
-- CMAKE_BINARY_DIR:/<<PKGBUILDDIR>>/build
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    DoublePrec_GPU


-- Build files have been written to: /<<PKGBUILDDIR>>/build
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -j4 -C build
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles /<<PKGBUILDDIR>>/build//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color=
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/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_printtable /<<PKGBUILDDIR>>/build/bin/relion_star_printtable
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cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /<<PKGBUILDDIR>>/build/macros.cpp
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_loopheader /<<PKGBUILDDIR>>/build/bin/relion_star_loopheader
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cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /<<PKGBUILDDIR>>/src/args.cpp
[  1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /<<PKGBUILDDIR>>/src/CPlot2D.cpp
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_stack /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_stack
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_singlefiles /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_singlefiles
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_ctfdat /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_ctfdat
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/qsub.csh /<<PKGBUILDDIR>>/build/bin/relion_qsub.csh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[  1%] Built target copy_scripts
[  1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o -MF CMakeFiles/relion_lib.dir/__/assembly.cpp.o.d -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /<<PKGBUILDDIR>>/src/assembly.cpp
[  2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /<<PKGBUILDDIR>>/src/autopicker.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/autopicker.h:10,
                 from /<<PKGBUILDDIR>>/src/autopicker.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/assembly.h:15,
                 from /<<PKGBUILDDIR>>/src/assembly.cpp:8:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Atom&}; _Tp = Atom; _Alloc = std::allocator<Atom>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Atom>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]',
    inlined from 'long int Residue::addAtom(std::string, double, double, double, double, double)' at /<<PKGBUILDDIR>>/src/assembly.cpp:36:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Atom*, std::vector<Atom> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]':
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/CPlot2D.h:30,
                 from /<<PKGBUILDDIR>>/src/CPlot2D.cpp:27:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataPoint>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:1617:35,
    inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/vector.tcc:232:44:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataSet>::iterator' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
    inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, std::vector<Residue> >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Molecule::Molecule(const Molecule&)' at /<<PKGBUILDDIR>>/src/assembly.h:118:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Molecule; _Args = {const Molecule&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const Molecule*; _ForwardIterator = Molecule*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Residue&}; _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/vector.tcc:462:28:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void CPlot2D::AddDataSet(std::vector<double>, std::vector<double>)' at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:503:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(std::vector<double>, std::vector<double>)' at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:505:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/stl_vector.h:1281:30,
    inlined from 'void Assembly::sortResidues()' at /<<PKGBUILDDIR>>/src/assembly.cpp:487:26:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
    inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = Residue*; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/vector.tcc:251:35,
    inlined from 'void Assembly::sortResidues()' at /<<PKGBUILDDIR>>/src/assembly.cpp:489:30:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void CPlot2D::AddDataSet(int, double*, double*)' at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:478:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(int, double*, double*)' at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:480:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/stl_vector.h:1281:30,
    inlined from 'long int Molecule::addResidue(Residue&)' at /<<PKGBUILDDIR>>/src/assembly.cpp:57:20:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void CPlot2D::AddDataSet(std::vector<double>)' at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:523:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(std::vector<double>)' at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:525:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[  2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/autopicker_mpi.cpp
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/stl_vector.h:1281:30,
    inlined from 'long int Molecule::addResidue(std::string, int)' at /<<PKGBUILDDIR>>/src/assembly.cpp:65:20:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
    inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, std::vector<Residue> >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Molecule::Molecule(const Molecule&)' at /<<PKGBUILDDIR>>/src/assembly.h:118:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Molecule&}; _Tp = Molecule; _Alloc = std::allocator<Molecule>]' at /usr/include/c++/12/bits/vector.tcc:462:28:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)':
/<<PKGBUILDDIR>>/src/CPlot2D.cpp:743:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
  743 |         sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac);
      |                                         ^~
/<<PKGBUILDDIR>>/src/CPlot2D.cpp:743:37: note: directive argument in the range [0, 2147483647]
  743 |         sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac);
      |                                     ^~~~~~~~
In file included from /usr/include/stdio.h:906,
                 from /usr/include/c++/12/cstdio:42,
                 from /usr/include/c++/12/ext/string_conversions.h:43,
                 from /usr/include/c++/12/bits/basic_string.h:3960,
                 from /usr/include/c++/12/string:53,
                 from /usr/include/c++/12/bits/locale_classes.h:40,
                 from /usr/include/c++/12/bits/ios_base.h:41,
                 from /usr/include/c++/12/ios:42,
                 from /usr/include/c++/12/ostream:38,
                 from /usr/include/c++/12/iostream:39,
                 from /<<PKGBUILDDIR>>/src/CPlot2D.cpp:21:
In function 'int sprintf(char*, const char*, ...)',
    inlined from 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)' at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:743:16:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)':
/<<PKGBUILDDIR>>/src/CPlot2D.cpp:733:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
  733 |         sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac);
      |                                         ^~
/<<PKGBUILDDIR>>/src/CPlot2D.cpp:733:37: note: directive argument in the range [0, 2147483647]
  733 |         sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac);
      |                                     ^~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
    inlined from 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)' at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:733:16:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
    inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, std::vector<Residue> >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Molecule::Molecule(const Molecule&)' at /<<PKGBUILDDIR>>/src/assembly.h:118:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Molecule; _Alloc = std::allocator<Molecule>]' at /usr/include/c++/12/bits/stl_vector.h:1281:30,
    inlined from 'long int Assembly::addMolecule(std::string, std::string)' at /<<PKGBUILDDIR>>/src/assembly.cpp:131:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[  3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /<<PKGBUILDDIR>>/src/backprojector.cpp
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/vector.tcc:145:30:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'std::vector<_Tp, _Alloc>::_Temporary_value::_Temporary_value(std::vector<_Tp, _Alloc>*, _Args&& ...) [with _Args = {const Residue&}; _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/stl_vector.h:1830:30,
    inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/vector.tcc:156:23:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {Residue}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {Residue}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'void std::vector<_Tp, _Alloc>::_M_insert_aux(iterator, _Arg&&) [with _Arg = Residue; _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/vector.tcc:417:31,
    inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/vector.tcc:157:19:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/stl_vector.h:1281:30,
    inlined from 'long int Molecule::addResidue(Residue&)' at /<<PKGBUILDDIR>>/src/assembly.cpp:57:20,
    inlined from 'void Molecule::insertResidues(Molecule, int, int)' at /<<PKGBUILDDIR>>/src/assembly.cpp:116:14:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
    inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, std::vector<Residue> >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Molecule::Molecule(const Molecule&)' at /<<PKGBUILDDIR>>/src/assembly.h:118:7,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Molecule; _Alloc = std::allocator<Molecule>]' at /usr/include/c++/12/bits/stl_vector.h:1281:30,
    inlined from 'long int Assembly::addMolecule(Molecule&)' at /<<PKGBUILDDIR>>/src/assembly.cpp:162:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/autopicker.h:10,
                 from /<<PKGBUILDDIR>>/src/autopicker_mpi.h:12,
                 from /<<PKGBUILDDIR>>/src/autopicker_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /<<PKGBUILDDIR>>/src/complex.cpp
[  3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctf.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /<<PKGBUILDDIR>>/src/ctf.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/backprojector.cpp:27:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /<<PKGBUILDDIR>>/src/ctffind_runner.cpp
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
                 from /usr/include/c++/12/algorithm:61,
                 from /<<PKGBUILDDIR>>/src/funcs.h:55,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPixel*, vector<ccfPixel> >; _Distance = int; _Tp = ccfPixel; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
  224 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/ctf.cpp:45:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPixel*, vector<ccfPixel> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
 1802 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPixel*, vector<ccfPixel> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
 1908 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
 1922 |           std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.h:31,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1782 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
[  4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/ctffind_runner_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.h:31,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o -MF CMakeFiles/relion_lib.dir/__/error.cpp.o.d -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /<<PKGBUILDDIR>>/src/error.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AmyloidCoord&}; _Tp = AmyloidCoord; _Alloc = std::allocator<AmyloidCoord>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<AmyloidCoord>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator<AmyloidCoord>]',
    inlined from 'std::vector<AmyloidCoord> AutoPicker::findNextCandidateCoordinates(AmyloidCoord&, std::vector<AmyloidCoord>&, double, double, int, float, MultidimArray<double>&, MultidimArray<double>&)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1092:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AmyloidCoord*, std::vector<AmyloidCoord> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[  5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o -MF CMakeFiles/relion_lib.dir/__/euler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /<<PKGBUILDDIR>>/src/euler.cpp
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator<AmyloidCoord>]',
    inlined from 'void AutoPicker::pickAmyloids(MultidimArray<double>&, MultidimArray<double>&, MultidimArray<double>&, MultidimArray<double>&, double, double, FileName&, FileName&, double, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1294:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AmyloidCoord*, std::vector<AmyloidCoord> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator<AmyloidCoord>]',
    inlined from 'void AutoPicker::pickAmyloids(MultidimArray<double>&, MultidimArray<double>&, MultidimArray<double>&, MultidimArray<double>&, double, double, FileName&, FileName&, double, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1321:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AmyloidCoord*, std::vector<AmyloidCoord> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator<AmyloidCoord>]',
    inlined from 'void AutoPicker::pickAmyloids(MultidimArray<double>&, MultidimArray<double>&, MultidimArray<double>&, MultidimArray<double>&, double, double, FileName&, FileName&, double, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1338:18:
/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AmyloidCoord*, std::vector<AmyloidCoord> >' changed in GCC 7.1
  164 |         _M_realloc_insert(begin() + (__position - cbegin()), __x);
      |         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator<AmyloidCoord>]',
    inlined from 'void AutoPicker::pickAmyloids(MultidimArray<double>&, MultidimArray<double>&, MultidimArray<double>&, MultidimArray<double>&, double, double, FileName&, FileName&, double, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1350:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AmyloidCoord*, std::vector<AmyloidCoord> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ccfPeak&}; _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<ccfPeak>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Peak&}; _Tp = Peak; _Alloc = std::allocator<Peak>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Peak>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator<Peak>]',
    inlined from 'void AutoPicker::prunePeakClusters(std::vector<Peak>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:3616:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Peak*, std::vector<Peak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator<Peak>]',
    inlined from 'void AutoPicker::prunePeakClusters(std::vector<Peak>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:3629:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Peak*, std::vector<Peak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator<Peak>]',
    inlined from 'void AutoPicker::prunePeakClusters(std::vector<Peak>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:3654:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Peak*, std::vector<Peak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator<Peak>]',
    inlined from 'void AutoPicker::removeTooCloselyNeighbouringPeaks(std::vector<Peak>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:3698:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Peak*, std::vector<Peak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[  5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/exp_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /<<PKGBUILDDIR>>/src/exp_model.cpp
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator<Peak>]',
    inlined from 'void AutoPicker::peakSearch(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, int, int, std::vector<Peak>&, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:3599:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Peak*, std::vector<Peak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {ccfPixel}; _Tp = ccfPixel; _Alloc = std::allocator<ccfPixel>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<ccfPixel>::iterator' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/exp_model.h:24,
                 from /<<PKGBUILDDIR>>/src/exp_model.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1802 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
[  6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -MF CMakeFiles/relion_lib.dir/__/fftw.cpp.o.d -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /<<PKGBUILDDIR>>/src/fftw.cpp
[  6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /<<PKGBUILDDIR>>/src/filename.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/multidim_array.h:52,
                 from /<<PKGBUILDDIR>>/src/fftw.h:50,
                 from /<<PKGBUILDDIR>>/src/fftw.cpp:47:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataPoint>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ccfPeak*, vector<ccfPeak> >; _ForwardIterator = ccfPeak*]':
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataSet>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void helicalLayerLineProfile(const MultidimArray<double>&, std::string, std::string)' at /<<PKGBUILDDIR>>/src/fftw.cpp:1725:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void helicalLayerLineProfile(const MultidimArray<double>&, std::string, std::string)' at /<<PKGBUILDDIR>>/src/fftw.cpp:1726:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void helicalLayerLineProfile(const MultidimArray<double>&, std::string, std::string)' at /<<PKGBUILDDIR>>/src/fftw.cpp:1741:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void helicalLayerLineProfile(const MultidimArray<double>&, std::string, std::string)' at /<<PKGBUILDDIR>>/src/fftw.cpp:1742:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[  6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /<<PKGBUILDDIR>>/src/flex_analyser.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/exp_model.h:24,
                 from /<<PKGBUILDDIR>>/src/flex_analyser.h:24,
                 from /<<PKGBUILDDIR>>/src/flex_analyser.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -MF CMakeFiles/relion_lib.dir/__/funcs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /<<PKGBUILDDIR>>/src/funcs.cpp
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void AutoPicker::initialise()' at /<<PKGBUILDDIR>>/src/autopicker.cpp:319:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void AutoPicker::initialise()' at /<<PKGBUILDDIR>>/src/autopicker.cpp:320:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void AutoPicker::initialise()' at /<<PKGBUILDDIR>>/src/autopicker.cpp:321:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void AutoPicker::initialise()' at /<<PKGBUILDDIR>>/src/autopicker.cpp:322:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void AutoPicker::initialise()' at /<<PKGBUILDDIR>>/src/autopicker.cpp:324:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[  7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -MF CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o.d -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /<<PKGBUILDDIR>>/src/healpix_sampling.cpp
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Distance = int; _Tp = ccfPeak; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
  224 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1625 |     __heap_select(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1908 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1922 |           std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1900 |       std::__heap_select(__first, __middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
                 from /usr/include/c++/12/algorithm:61,
                 from /<<PKGBUILDDIR>>/src/funcs.h:55,
                 from /<<PKGBUILDDIR>>/src/matrix1d.h:48,
                 from /<<PKGBUILDDIR>>/src/matrix2d.h:50,
                 from /<<PKGBUILDDIR>>/src/exp_model.h:23:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  224 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1802 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1908 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1922 |           std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ccfPixel}; _Tp = ccfPixel; _Alloc = std::allocator<ccfPixel>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ccfPixel; _Alloc = std::allocator<ccfPixel>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<int>&, double, int, double, std::vector<ccfPeak>&, MultidimArray<double>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1526:29:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPixel*, vector<ccfPixel> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<ccfPixel*, vector<ccfPixel> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<int>&, double, int, double, std::vector<ccfPeak>&, MultidimArray<double>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1530:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPixel*, vector<ccfPixel> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPixel*, vector<ccfPixel> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<ccfPixel*, vector<ccfPixel> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<int>&, double, int, double, std::vector<ccfPeak>&, MultidimArray<double>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1530:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
 1849 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
 1854 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ccfPixel}; _Tp = ccfPixel; _Alloc = std::allocator<ccfPixel>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ccfPixel; _Alloc = std::allocator<ccfPixel>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<int>&, double, int, double, std::vector<ccfPeak>&, MultidimArray<double>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1624:44:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPixel*, std::vector<ccfPixel> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<int>&, double, int, double, std::vector<ccfPeak>&, MultidimArray<double>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1675:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<int>&, double, int, double, std::vector<ccfPeak>&, MultidimArray<double>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1680:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<int>&, double, int, double, std::vector<ccfPeak>&, MultidimArray<double>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1680:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1849 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1854 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<int>&, double, int, double, std::vector<ccfPeak>&, MultidimArray<double>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1738:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ccfPeak*, std::vector<ccfPeak> >; _ForwardIterator = ccfPeak*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ccfPeak*, vector<ccfPeak> >; _ForwardIterator = ccfPeak*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const ccfPeak*, vector<ccfPeak> >; _ForwardIterator = ccfPeak*; _Tp = ccfPeak]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const ccfPeak*, std::vector<ccfPeak> >; _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]' at /usr/include/c++/12/bits/stl_vector.h:1617:35,
    inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]' at /usr/include/c++/12/bits/vector.tcc:232:44,
    inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<double>&, const MultidimArray<int>&, double, int, double, std::vector<ccfPeak>&, MultidimArray<double>&, int, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1741:18:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix.h:30,
                 from /<<PKGBUILDDIR>>/src/healpix_sampling.h:31,
                 from /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1809:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1809:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1849 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1854 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1856:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1924:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1929:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:1964:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:2035:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:2104:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:2174:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:2218:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:2219:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:2221:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:2275:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)' at /<<PKGBUILDDIR>>/src/autopicker.cpp:2293:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataPoint>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataSet>::iterator' changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
[  7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /<<PKGBUILDDIR>>/src/helix.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/Healpix_2.15a/healpix_base.h:35,
                 from /<<PKGBUILDDIR>>/src/healpix_sampling.h:24:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:417:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:420:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:421:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:425:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:426:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:436:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:437:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::addOneTranslation(double, double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:469:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::addOneTranslation(double, double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:470:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::addOneTranslation(double, double, double, bool, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:472:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1923:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1924:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1925:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1933:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1934:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1937:50:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::getOrientations(long int, long int, int, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1844:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::getOrientations(long int, long int, int, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1845:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::getOrientations(long int, long int, int, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1846:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix.h:30,
                 from /<<PKGBUILDDIR>>/src/helix.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::findSymmetryMate(long int, double, std::vector<int>&, std::vector<double>&, std::vector<bool>&)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1096:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::removePointsOutsideLimitedTiltAngles()' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:2101:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::removePointsOutsideLimitedTiltAngles()' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:2102:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1758:34:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1759:34:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1760:34:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1765:33:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1766:33:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:572:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:573:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:578:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:579:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:584:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1365:31:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1381:30:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1397:29:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1436:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1469:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:846:31:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:922:31:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:938:29:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:968:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:992:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[  8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:564:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:567:13:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:567:13:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1849 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1854 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix_inimodel2d.h:29,
                 from /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/algorithm:61,
                 from /<<PKGBUILDDIR>>/src/funcs.h:55,
                 from /<<PKGBUILDDIR>>/src/multidim_array.h:52,
                 from /<<PKGBUILDDIR>>/src/helix.h:26:
/usr/include/c++/12/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >]':
/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 1281 |     __rotate(_RandomAccessIterator __first,
      |     ^~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::removeSymmetryEquivalentPoints(double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:2205:38:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::removeSymmetryEquivalentPoints(double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:2206:39:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setOrientations(int, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:501:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setOrientations(int, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:502:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::setOrientations(int, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:531:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HealpixSampling::setOrientations(int, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:532:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HealpixSampling::setOrientations(int, double)' at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:548:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:471:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:472:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:473:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:474:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:476:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:509:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:512:13:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:512:13:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1849 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1854 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:535:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:536:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:537:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:538:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:544:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[  8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -MF CMakeFiles/relion_lib.dir/__/image.cpp.o.d -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /<<PKGBUILDDIR>>/src/image.cpp
/usr/include/c++/12/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = HelicalSegmentPriorInfoEntry*; _OutputIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2615 |     __move_merge(_InputIterator __first1, _InputIterator __last1,
      |     ^~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _OutputIterator = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 1802 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2682 |     __merge_sort_with_buffer(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
In function 'void std::__chunk_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2693:34:
/usr/include/c++/12/bits/stl_algo.h:2672:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2672 |           std::__insertion_sort(__first, __first + __chunk_size, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2675 |       std::__insertion_sort(__first, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _RandomAccessIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2697:26:
/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2650 |           __result = std::__move_merge(__first, __first + __step_size,
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2651 |                                        __first + __step_size,
      |                                        ~~~~~~~~~~~~~~~~~~~~~~
 2652 |                                        __first + __two_step,
      |                                        ~~~~~~~~~~~~~~~~~~~~~
 2653 |                                        __result, __comp);
      |                                        ~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2658 |       std::__move_merge(__first, __first + __step_size,
      |       ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2659 |                         __first + __step_size, __last, __result, __comp);
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = HelicalSegmentPriorInfoEntry*; _RandomAccessIterator2 = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2700:26:
/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2650 |           __result = std::__move_merge(__first, __first + __step_size,
      |                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2651 |                                        __first + __step_size,
      |                                        ~~~~~~~~~~~~~~~~~~~~~~
 2652 |                                        __first + __two_step,
      |                                        ~~~~~~~~~~~~~~~~~~~~~
 2653 |                                        __result, __comp);
      |                                        ~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2658 |       std::__move_merge(__first, __first + __step_size,
      |       ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2659 |                         __first + __step_size, __last, __result, __comp);
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/image.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /<<PKGBUILDDIR>>/src/local_symmetry.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/time.h:31,
                 from /<<PKGBUILDDIR>>/src/helix_inimodel2d.h:26:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const fit_point3D&}; _Tp = fit_point3D; _Alloc = std::allocator<fit_point3D>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<fit_point3D>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fit_point3D; _Alloc = std::allocator<fit_point3D>]',
    inlined from 'void subtractBackgroundRamp(Image<double>&, int, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/image.cpp:307:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fit_point3D*, std::vector<fit_point3D> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fit_point3D; _Alloc = std::allocator<fit_point3D>]',
    inlined from 'void subtractBackgroundRamp(Image<double>&, int, bool, double, double, double)' at /<<PKGBUILDDIR>>/src/image.cpp:323:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fit_point3D*, std::vector<fit_point3D> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.h:30,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
[  9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/local_symmetry_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.h:30,
                 from /<<PKGBUILDDIR>>/src/local_symmetry_mpi.h:5,
                 from /<<PKGBUILDDIR>>/src/local_symmetry_mpi.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:4957:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:4958:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:4959:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2051:61:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2052:61:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2053:62:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2054:62:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2055:71:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2056:56:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2057:75:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2058:69:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2059:56:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2060:65:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2062:60:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2064:69:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2066:66:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2068:70:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /<<PKGBUILDDIR>>/src/helix.cpp:2070:71:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HelixAligner::readImages()' at /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp:337:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HelixAligner::readImages()' at /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp:338:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void HelixAligner::readImages()' at /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp:363:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HelixAligner::readImages()' at /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp:372:34:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:1867:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:1868:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:1877:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:1882:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:1883:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void HelixAlignerModel::initialise(int, int, int)' at /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp:37:16:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {HelicalSymmetryItem}; _Tp = HelicalSymmetryItem; _Alloc = std::allocator<HelicalSymmetryItem>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<HelicalSymmetryItem>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {HelicalSymmetryItem}; _Tp = HelicalSymmetryItem; _Alloc = std::allocator<HelicalSymmetryItem>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = HelicalSymmetryItem; _Alloc = std::allocator<HelicalSymmetryItem>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void makeHelicalSymmetryList(std::vector<HelicalSymmetryItem>&, double, double, double, bool, double, double, double, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:69:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSymmetryItem*, std::vector<HelicalSymmetryItem> >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:61:
/usr/include/c++/12/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >; _Tp = HelicalSegmentPriorInfoEntry]':
/usr/include/c++/12/bits/stl_tempbuf.h:258:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
  258 |     _Temporary_buffer<_ForwardIterator, _Tp>::
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/args.h:52,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.h:24:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
[  9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /<<PKGBUILDDIR>>/src/mask.cpp
[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /<<PKGBUILDDIR>>/src/matrix1d.cpp
[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /<<PKGBUILDDIR>>/src/matrix2d.cpp
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:5283:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:5293:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:5295:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:5305:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:5307:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:5334:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:5335:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /<<PKGBUILDDIR>>/src/helix.cpp:5336:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -MF CMakeFiles/relion_lib.dir/__/memory.cpp.o.d -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /<<PKGBUILDDIR>>/src/memory.cpp
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /<<PKGBUILDDIR>>/src/metadata_container.cpp
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /<<PKGBUILDDIR>>/src/metadata_label.cpp
/usr/include/c++/12/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _BidirectionalIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int]':
/usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2352 |     __rotate_adaptive(_BidirectionalIterator1 __first,
      |     ^~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >]',
    inlined from '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _BidirectionalIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int]' at /usr/include/c++/12/bits/stl_algo.h:2383:20:
/usr/include/c++/12/bits/stl_algo.h:1397:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 1397 |       return std::__rotate(__first, __middle, __last,
      |              ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 1398 |                            std::__iterator_category(__first));
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2390 |     __merge_adaptive(_BidirectionalIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2435:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2435 |             = std::__rotate_adaptive(__first_cut, __middle, __second_cut,
      |               ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2436 |                                      __len1 - __len11, __len22, __buffer,
      |                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2437 |                                      __buffer_size);
      |                                      ~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2438:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2438 |           std::__merge_adaptive(__first, __first_cut, __new_middle, __len11,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2439 |                                 __len22, __buffer, __buffer_size, __comp);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2440:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2440 |           std::__merge_adaptive(__new_middle, __second_cut, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2441 |                                 __len1 - __len11,
      |                                 ~~~~~~~~~~~~~~~~~
 2442 |                                 __len2 - __len22, __buffer,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2443 |                                 __buffer_size, __comp);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:2709:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2709 |     __stable_sort_adaptive(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2709:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2718:38: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2718 |           std::__stable_sort_adaptive(__first, __middle, __buffer,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2719 |                                       __buffer_size, __comp);
      |                                       ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2720:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2720 |           std::__stable_sort_adaptive(__middle, __last, __buffer,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2721 |                                       __buffer_size, __comp);
      |                                       ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2725:40: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2725 |           std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2726:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2726 |           std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2729:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2729 |       std::__merge_adaptive(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2730 |                             _Distance(__middle - __first),
      |                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2731 |                             _Distance(__last - __middle),
      |                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2732 |                             __buffer, __buffer_size,
      |                             ~~~~~~~~~~~~~~~~~~~~~~~~
 2733 |                             __comp);
      |                             ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:2451:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2451 |     __merge_without_buffer(_BidirectionalIterator __first,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2451:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2451:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >]',
    inlined from 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2491:15:
/usr/include/c++/12/bits/stl_algo.h:1397:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 1397 |       return std::__rotate(__first, __middle, __last,
      |              ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 1398 |                            std::__iterator_category(__first));
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:2492:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2492 |       std::__merge_without_buffer(__first, __first_cut, __new_middle,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2493 |                                   __len11, __len22, __comp);
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2494:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2494 |       std::__merge_without_buffer(__new_middle, __second_cut, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2495 |                                   __len1 - __len11, __len2 - __len22, __comp);
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:2739:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2739 |     __inplace_stable_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2739:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2748 |       std::__inplace_stable_sort(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2749 |       std::__inplace_stable_sort(__middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2748 |       std::__inplace_stable_sort(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2748 |       std::__inplace_stable_sort(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2749 |       std::__inplace_stable_sort(__middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2748 |       std::__inplace_stable_sort(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2749 |       std::__inplace_stable_sort(__middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2748 |       std::__inplace_stable_sort(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2749 |       std::__inplace_stable_sort(__middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2748 |       std::__inplace_stable_sort(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2749 |       std::__inplace_stable_sort(__middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2748 |       std::__inplace_stable_sort(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2749 |       std::__inplace_stable_sort(__middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2748 |       std::__inplace_stable_sort(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2749 |       std::__inplace_stable_sort(__middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2744 |           std::__insertion_sort(__first, __last, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2748 |       std::__inplace_stable_sort(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2749 |       std::__inplace_stable_sort(__middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33,
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 2750 |       std::__merge_without_buffer(__first, __middle, __last,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
 2751 |                                   __middle - __first,
      |                                   ~~~~~~~~~~~~~~~~~~~
 2752 |                                   __last - __middle,
      |                                   ~~~~~~~~~~~~~~~~~~
 2753 |                                   __comp);
      |                                   ~~~~~~~
[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /<<PKGBUILDDIR>>/src/metadata_table.cpp
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const HelicalSegmentPriorInfoEntry&}; _Tp = HelicalSegmentPriorInfoEntry; _Alloc = std::allocator<HelicalSegmentPriorInfoEntry>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<HelicalSegmentPriorInfoEntry>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = HelicalSegmentPriorInfoEntry; _Alloc = std::allocator<HelicalSegmentPriorInfoEntry>]',
    inlined from 'void updatePriorsForHelicalReconstruction(MetaDataTable&, double, std::vector<double, std::allocator<double> >, std::vector<double, std::allocator<double> >, int, bool, bool, double, double, double, double, bool, int)' at /<<PKGBUILDDIR>>/src/helix.cpp:4475:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >]' at /usr/include/c++/12/bits/stl_algo.h:5034:36,
    inlined from 'void updatePriorsForHelicalReconstruction(MetaDataTable&, double, std::vector<double, std::allocator<double> >, std::vector<double, std::allocator<double> >, int, bool, bool, double, double, double, double, bool, int)' at /<<PKGBUILDDIR>>/src/helix.cpp:4479:18:
/usr/include/c++/12/bits/stl_algo.h:4996:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 4996 |       _TmpBuf __buf(__first, (__last - __first + 1) / 2);
      |               ^~~~~
/usr/include/c++/12/bits/stl_algo.h:4999:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 4999 |         std::__inplace_stable_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:5001:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >' changed in GCC 7.1
 5001 |         std::__stable_sort_adaptive(__first, __last, __buf.begin(),
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5002 |                                     _DistanceType(__buf.size()), __comp);
      |                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]':
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:1617:35,
    inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/vector.tcc:232:44:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
    inlined from 'Residue::Residue(const Residue&)' at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
    inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7,
    inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
    inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = Residue*; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]' at /usr/include/c++/12/bits/vector.tcc:251:35:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1550:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1553:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1557:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1560:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1564:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1567:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1577:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1580:16:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1585:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1588:16:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1593:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1596:16:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
                 from /usr/include/c++/12/algorithm:61,
                 from /<<PKGBUILDDIR>>/src/funcs.h:55,
                 from /<<PKGBUILDDIR>>/src/metadata_table.h:43,
                 from /<<PKGBUILDDIR>>/src/metadata_table.cpp:45:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  224 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Distance = int; _Tp = pair<double, long int>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1802 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1908 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1922 |           std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
 1908 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
 1922 |           std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
 1802 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /<<PKGBUILDDIR>>/src/micrograph_model.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/metadata_table.h:33:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataPoint>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataSet>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1528:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1532:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  523 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/micrograph_model.cpp:23:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1363:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1363:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1849 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1854 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1407:14:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1408:14:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1363:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MetaDataTable::columnHistogram(EMDLabel, std::vector<double>&, std::vector<double>&, int, CPlot2D*, long int, double, double, bool, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1341:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<double, long int>}; _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<std::pair<double, long int> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, long int>}; _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void MetaDataTable::sort(EMDLabel, bool, bool, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:508:15:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void MetaDataTable::sort(EMDLabel, bool, bool, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:512:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void MetaDataTable::sort(EMDLabel, bool, bool, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:512:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
 1849 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >' changed in GCC 7.1
 1854 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'bool MetaDataTable::setValueFromString(EMDLabel, const std::string&, long int)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:385:16:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/micrograph_model.h:23,
                 from /<<PKGBUILDDIR>>/src/micrograph_model.cpp:21:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  523 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'MetaDataTable removeDuplicatedParticles(MetaDataTable&, EMDLabel, double, double, FileName, bool)' at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1885:19:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Micrograph::read(FileName, bool)' at /<<PKGBUILDDIR>>/src/micrograph_model.cpp:454:21:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Micrograph::read(FileName, bool)' at /<<PKGBUILDDIR>>/src/micrograph_model.cpp:455:21:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /<<PKGBUILDDIR>>/src/ml_model.cpp
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Micrograph::setMovie(FileName, FileName, double)' at /<<PKGBUILDDIR>>/src/micrograph_model.cpp:575:21:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Micrograph::setMovie(FileName, FileName, double)' at /<<PKGBUILDDIR>>/src/micrograph_model.cpp:576:21:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_model.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /<<PKGBUILDDIR>>/src/ml_optimiser.cpp
[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:44:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.h:24,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/multidim_array.h:52,
                 from /<<PKGBUILDDIR>>/src/fftw.h:50,
                 from /<<PKGBUILDDIR>>/src/projector.h:23:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  523 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
                 from /usr/include/c++/12/algorithm:61,
                 from /<<PKGBUILDDIR>>/src/funcs.h:55,
                 from /<<PKGBUILDDIR>>/src/multidim_array.h:52,
                 from /<<PKGBUILDDIR>>/src/fftw.h:50,
                 from /<<PKGBUILDDIR>>/src/projector.h:23:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  224 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1802 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1908 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1922 |           std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<BackProjector*>; _ForwardIterator = BackProjector*]':
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type 'std::move_iterator<BackProjector*>' changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type 'std::move_iterator<BackProjector*>' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlModel::initialiseBodies(FileName, FileName, bool, int)' at /<<PKGBUILDDIR>>/src/ml_model.cpp:1085:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlModel::initialiseBodies(FileName, FileName, bool, int)' at /<<PKGBUILDDIR>>/src/ml_model.cpp:1086:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlModel::initialiseBodies(FileName, FileName, bool, int)' at /<<PKGBUILDDIR>>/src/ml_model.cpp:1087:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlModel::initialiseBodies(FileName, FileName, bool, int)' at /<<PKGBUILDDIR>>/src/ml_model.cpp:1088:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlModel::initialise(bool)' at /<<PKGBUILDDIR>>/src/ml_model.cpp:45:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:33:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  523 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlModel::read(FileName)' at /<<PKGBUILDDIR>>/src/ml_model.cpp:341:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator<BackProjector>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<BackProjector>::iterator' changed in GCC 7.1
  523 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<BackProjector*>; _ForwardIterator = BackProjector*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<BackProjector*>; _ForwardIterator = BackProjector*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<BackProjector*>; _ForwardIterator = BackProjector*; _Tp = BackProjector]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = BackProjector*; _ForwardIterator = BackProjector*; _Allocator = allocator<BackProjector>]' at /usr/include/c++/12/bits/stl_uninitialized.h:382:41,
    inlined from 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator<BackProjector>]' at /usr/include/c++/12/bits/vector.tcc:542:32:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type 'std::move_iterator<BackProjector*>' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<BackProjector*>; _ForwardIterator = BackProjector*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<BackProjector*>; _ForwardIterator = BackProjector*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<BackProjector*>; _ForwardIterator = BackProjector*; _Tp = BackProjector]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
    inlined from '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = BackProjector*; _ForwardIterator = BackProjector*; _Allocator = allocator<BackProjector>]' at /usr/include/c++/12/bits/stl_uninitialized.h:382:41,
    inlined from 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator<BackProjector>]' at /usr/include/c++/12/bits/vector.tcc:562:32:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type 'std::move_iterator<BackProjector*>' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator<BackProjector>]',
    inlined from 'void MlWsumModel::initialise(MlModel&, FileName, bool, bool)' at /<<PKGBUILDDIR>>/src/ml_model.cpp:1503:14:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BackProjector*, std::vector<BackProjector> >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void MlOptimiser::maximizationOtherParameters()' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:4255:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void MlOptimiser::maximizationOtherParameters()' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:4255:12:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1849 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1854 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.h:32,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/motioncorr_runner_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.h:32,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /<<PKGBUILDDIR>>/src/mpi.cpp
[ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -MF CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o.d -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /<<PKGBUILDDIR>>/src/multidim_array.cpp
[ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -MF CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o.d -o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -c /<<PKGBUILDDIR>>/src/numerical_recipes.cpp
In file included from /<<PKGBUILDDIR>>/src/numerical_recipes.h:48,
                 from /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:49:
In function 'void free_Tvector(T*&, int, int) [with T = double]',
    inlined from 'double brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)' at /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:594:25:
/<<PKGBUILDDIR>>/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xt' with nonzero offset 8 [-Wfree-nonheap-object]
   74 |         free((char*)(v + nl));
      |         ~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp: In function 'double brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp:579:13: note: declared here
  579 |     RFLOAT *xt=NULL;
      |             ^~
[ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /<<PKGBUILDDIR>>/src/parallel.cpp
In function 'void free_Tvector(T*&, int, int) [with T = double]',
    inlined from 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)' at /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:767:25:
/<<PKGBUILDDIR>>/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xit' with nonzero offset 8 [-Wfree-nonheap-object]
   74 |         free((char*)(v + nl));
      |         ~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp: In function 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)':
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp:703:24: note: declared here
  703 |     RFLOAT *pt, *ptt, *xit;
      |                        ^~~
In function 'void free_Tvector(T*&, int, int) [with T = double]',
    inlined from 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)' at /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:768:25:
/<<PKGBUILDDIR>>/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'ptt' with nonzero offset 8 [-Wfree-nonheap-object]
   74 |         free((char*)(v + nl));
      |         ~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp: In function 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)':
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp:703:18: note: declared here
  703 |     RFLOAT *pt, *ptt, *xit;
      |                  ^~~
In function 'void free_Tvector(T*&, int, int) [with T = double]',
    inlined from 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)' at /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:769:25:
/<<PKGBUILDDIR>>/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'pt' with nonzero offset 8 [-Wfree-nonheap-object]
   74 |         free((char*)(v + nl));
      |         ~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp: In function 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)':
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp:703:13: note: declared here
  703 |     RFLOAT *pt, *ptt, *xit;
      |             ^~
[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /<<PKGBUILDDIR>>/src/particle_subtractor.cpp
[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /<<PKGBUILDDIR>>/src/pipeline_control.cpp
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::initialiseGeneral(int)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:1933:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::initialiseGeneral(int)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:1934:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::initialiseGeneral(int)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:1938:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.h:25:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataPoint>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataSet>::iterator' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/particle_subtractor.h:24,
                 from /<<PKGBUILDDIR>>/src/particle_subtractor.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /<<PKGBUILDDIR>>/src/pipeline_jobs.cpp
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray<double>&, MultidimArray<bool>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<Matrix1D<double> >&, std::vector<Matrix1D<double> >&, std::vector<double, std::allocator<double> >&, std::vector<int>&, std::vector<int>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:6682:23:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray<double>&, MultidimArray<bool>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<Matrix1D<double> >&, std::vector<Matrix1D<double> >&, std::vector<double, std::allocator<double> >&, std::vector<int>&, std::vector<int>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:7049:31:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:737:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:740:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:749:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:750:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:776:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:778:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:779:44:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:782:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:783:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:785:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::expectationSomeParticles(long int, long int)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:3402:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::getAllSquaredDifferences(long int, int, int, int, int, int, int, int, int, int, int, int, int, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<MultidimArray<tComplex<double> > >&, std::vector<MultidimArray<double> >&, MultidimArray<double>&, MultidimArray<bool>&, std::vector<int>&, std::vector<int>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<MultidimArray<tComplex<double> > > >&, std::vector<MultidimArray<double> >&, std::vector<MultidimArray<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:6108:22:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:1442:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:1443:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:1453:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<MultidimArray<tComplex<double> > >&, std::vector<MultidimArray<tComplex<double> > >&, std::vector<MultidimArray<double> >&, std::vector<MultidimArray<double> >&, std::vector<Matrix1D<double> >&, std::vector<Matrix1D<double> >&, MultidimArray<double>&, MultidimArray<bool>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<int>&, std::vector<int>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<MultidimArray<tComplex<double> > > >&, std::vector<std::vector<MultidimArray<tComplex<double> > > >&, std::vector<MultidimArray<double> >&, std::vector<MultidimArray<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:7233:23:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<MultidimArray<tComplex<double> > >&, std::vector<MultidimArray<tComplex<double> > >&, std::vector<MultidimArray<double> >&, std::vector<MultidimArray<double> >&, std::vector<Matrix1D<double> >&, std::vector<Matrix1D<double> >&, MultidimArray<double>&, MultidimArray<bool>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<int>&, std::vector<int>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<MultidimArray<tComplex<double> > > >&, std::vector<std::vector<MultidimArray<tComplex<double> > > >&, std::vector<MultidimArray<double> >&, std::vector<MultidimArray<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:7315:23:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<MultidimArray<tComplex<double> > >&, std::vector<MultidimArray<tComplex<double> > >&, std::vector<MultidimArray<double> >&, std::vector<MultidimArray<double> >&, std::vector<Matrix1D<double> >&, std::vector<Matrix1D<double> >&, MultidimArray<double>&, MultidimArray<bool>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<int>&, std::vector<int>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<MultidimArray<tComplex<double> > > >&, std::vector<std::vector<MultidimArray<tComplex<double> > > >&, std::vector<MultidimArray<double> >&, std::vector<MultidimArray<double> >&, std::vector<double, std::allocator<double> >&)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:7317:27:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /<<PKGBUILDDIR>>/src/pipeliner.cpp
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MlOptimiser::expectationOneParticle(long int, int)' at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:3741:32:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /<<PKGBUILDDIR>>/src/postprocessing.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/postprocessing.h:24,
                 from /<<PKGBUILDDIR>>/src/postprocessing.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const fit_point2D&}; _Tp = fit_point2D; _Alloc = std::allocator<fit_point2D>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<fit_point2D>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fit_point2D; _Alloc = std::allocator<fit_point2D>]',
    inlined from 'void Postprocessing::makeGuinierPlot(MultidimArray<tComplex<double> >&, std::vector<fit_point2D>&)' at /<<PKGBUILDDIR>>/src/postprocessing.cpp:652:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<fit_point2D*, std::vector<fit_point2D> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /<<PKGBUILDDIR>>/src/preprocessing.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
                 from /<<PKGBUILDDIR>>/src/preprocessing.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/preprocessing_mpi.cpp
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void Postprocessing::run_locres(int, int)' at /<<PKGBUILDDIR>>/src/postprocessing.cpp:1139:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
                 from /<<PKGBUILDDIR>>/src/preprocessing_mpi.h:24,
                 from /<<PKGBUILDDIR>>/src/preprocessing_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /<<PKGBUILDDIR>>/src/projector.cpp
[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /<<PKGBUILDDIR>>/src/reconstructor.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/projector.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/reconstructor.h:23,
                 from /<<PKGBUILDDIR>>/src/reconstructor.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/reconstructor_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/reconstructor.h:23,
                 from /<<PKGBUILDDIR>>/src/reconstructor_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/reconstructor_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /<<PKGBUILDDIR>>/src/renderEER.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/renderEER.cpp:10:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/renderEER.cpp: In member function 'void EERRenderer::readLegacy(FILE*)':
/<<PKGBUILDDIR>>/src/renderEER.cpp:191:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  191 |         fread(buf, sizeof(char), file_size, fh);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /<<PKGBUILDDIR>>/src/scheduler.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/renderEER.cpp:4:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
    inlined from 'void EERRenderer::readLegacy(FILE*)' at /<<PKGBUILDDIR>>/src/renderEER.cpp:205:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
    inlined from 'void EERRenderer::readLegacy(FILE*)' at /<<PKGBUILDDIR>>/src/renderEER.cpp:206:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
  523 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
    inlined from 'void EERRenderer::lazyReadFrames()' at /<<PKGBUILDDIR>>/src/renderEER.cpp:230:23:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator<long long int>]',
    inlined from 'void EERRenderer::lazyReadFrames()' at /<<PKGBUILDDIR>>/src/renderEER.cpp:231:22:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:26,
                 from /<<PKGBUILDDIR>>/src/scheduler.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /<<PKGBUILDDIR>>/src/strings.cpp
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
                 from /usr/include/c++/12/algorithm:61,
                 from /<<PKGBUILDDIR>>/src/funcs.h:55,
                 from /<<PKGBUILDDIR>>/src/metadata_table.h:43,
                 from /<<PKGBUILDDIR>>/src/pipeliner.h:30,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:25:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >; _Distance = int; _Tp = pair<double, long int>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
  224 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
 1908 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
 1922 |           std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
 1802 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -MF CMakeFiles/relion_lib.dir/__/symmetries.cpp.o.d -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /<<PKGBUILDDIR>>/src/symmetries.cpp
[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /<<PKGBUILDDIR>>/src/tabfuncs.cpp
[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /<<PKGBUILDDIR>>/src/tiff_converter.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/tiff_converter.cpp:24:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function 'void TIFFConverter::estimate(FileName)':
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:141:101: warning: format '%d' expects argument of type 'int', but argument 7 has type 'long int' [-Wformat=]
  141 |                 printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n",
      |                                                                                                  ~~~^
      |                                                                                                     |
      |                                                                                                     int
      |                                                                                                  %10ld
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:141:108: warning: format '%d' expects argument of type 'int', but argument 8 has type 'long int' [-Wformat=]
  141 |                 printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n",
      |                                                                                                         ~~~^
      |                                                                                                            |
      |                                                                                                            int
      |                                                                                                         %10ld
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function 'int TIFFConverter::checkMRCtype(FileName)':
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:309:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  309 |         fread(headers, sizeof(int), 24, mrcin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function 'void TIFFConverter::initialise(int, int)':
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:367:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  367 |                 system(("mkdir -p " + fn_out.beforeLastOf("/")).c_str());
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function 'void TIFFConverter::run()':
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:530:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  530 |                         system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str());
      |                         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
                 from /<<PKGBUILDDIR>>/src/metadata_table.h:32:
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
 2457 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
/usr/include/c++/12/bits/stl_map.h: In function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]':
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
  511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  512 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  513 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]',
    inlined from 'float Schedule::getFloatVariableValue(std::string)' at /<<PKGBUILDDIR>>/src/scheduler.cpp:1080:37:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
  511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  512 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  513 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]',
    inlined from 'float Schedule::getFloatOriginalVariableValue(std::string)' at /<<PKGBUILDDIR>>/src/scheduler.cpp:1087:37:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
  511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  512 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  513 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]',
    inlined from 'void Schedule::setFloatOriginalVariableValue(std::string, double)' at /<<PKGBUILDDIR>>/src/scheduler.cpp:1102:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
  511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  512 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  513 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]',
    inlined from 'void Schedule::addFloatVariable(std::string, double)' at /<<PKGBUILDDIR>>/src/scheduler.cpp:1055:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
  511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  512 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  513 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]',
    inlined from 'void Schedule::setFloatVariableValue(std::string, double)' at /<<PKGBUILDDIR>>/src/scheduler.cpp:1094:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
  511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  512 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  513 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]',
    inlined from 'void Schedule::setFloatVariableValue(std::string, double)' at /<<PKGBUILDDIR>>/src/scheduler.cpp:1095:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
  511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  512 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  513 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/time.h:31,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:24:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<double, long int>}; _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, long int>}; _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void MultidimArray<T>::sorted_index(MultidimArray<long int>&) const [with T = double]' at /<<PKGBUILDDIR>>/src/multidim_array.h:3618:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void MultidimArray<T>::sorted_index(MultidimArray<long int>&) const [with T = double]' at /<<PKGBUILDDIR>>/src/multidim_array.h:3621:18:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
 1937 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1938 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1939 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
    inlined from 'void MultidimArray<T>::sorted_index(MultidimArray<long int>&) const [with T = double]' at /<<PKGBUILDDIR>>/src/multidim_array.h:3621:18:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
 1849 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >' changed in GCC 7.1
 1854 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /<<PKGBUILDDIR>>/src/time.cpp
[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o -MF CMakeFiles/relion_lib.dir/__/transformations.cpp.o.d -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /<<PKGBUILDDIR>>/src/transformations.cpp
[ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /<<PKGBUILDDIR>>/src/Healpix_2.15a/cxxutils.cc
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]',
    inlined from 'void Schedule::read(bool, FileName)' at /<<PKGBUILDDIR>>/src/scheduler.cpp:684:33:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
  511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  512 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  513 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]',
    inlined from 'void Schedule::setVariablesInJob(RelionJob&, FileName, bool&)' at /<<PKGBUILDDIR>>/src/scheduler.cpp:1628:59:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1
  511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  512 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  513 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
[ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /<<PKGBUILDDIR>>/src/Healpix_2.15a/healpix_base.cc
[ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/Fourier_helper.cpp
[ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/Gaussian_pyramid.cpp
[ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/aberration_fit.cpp
[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/complex_io.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/Fourier_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/Fourier_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/aberration_fit.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/aberration_fit.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/convolution_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/complex_io.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/complex_io.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/convolution_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/convolution_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/damage_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/fsc_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/damage_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/distribution_helper.cpp
[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/fftw_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/distribution_helper.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/distribution_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/fsc_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/fsc_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/fsc_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/image_log.cpp
[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/interpolation.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/image_log.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/image_log.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/interpolation.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/interpolation.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/jaz_config.cpp
[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/legacy_obs_model.cpp
[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/local_motion_fit.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/legacy_obs_model.h:4,
                 from /<<PKGBUILDDIR>>/src/jaz/legacy_obs_model.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/micrograph_handler.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/local_motion_fit.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/local_motion_fit.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/new_ft.cpp
[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/noise_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/micrograph_handler.h:31,
                 from /<<PKGBUILDDIR>>/src/jaz/micrograph_handler.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/obs_model.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/noise_helper.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/noise_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/jaz/noise_helper.h:24:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/parallel_ft.cpp
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static Image<double> NoiseHelper::predictCCNoise(Projector&, double, double, int, int, Image<double>&, CTF, double, double, double, int)' at /<<PKGBUILDDIR>>/src/jaz/noise_helper.cpp:134:40:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/reference_map.cpp
[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/refinement_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/refinement_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/refinement_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/resampling_helper.cpp
[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/slice_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/reference_map.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/reference_map.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/slice_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/slice_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/spectral_helper.cpp
[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/stack_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/spectral_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/spectral_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/stack_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/stack_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/structure_tensor.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/structure_tensor.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/svd_helper.cpp
[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/t_complex.cpp
[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/volume_converter.cpp
[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/volume_integration.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/volume_converter.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/volume_converter.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/volume_integration.h:26,
                 from /<<PKGBUILDDIR>>/src/jaz/volume_integration.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/vtk_helper.cpp
[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/gradient_descent.cpp
[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/lbfgs.cpp
[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/nelder_mead.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/vtk_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/vtk_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/optimization.cpp
[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.cpp
[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.h:4,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.h:4,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataPoint>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataSet>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void BFactorRefiner::writePerParticleEPS(const MetaDataTable&)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:474:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void BFactorRefiner::writePerParticleEPS(const MetaDataTable&)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:476:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, int)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:405:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, int)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:419:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, int)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:421:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, int)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:425:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void BFactorRefiner::writePerMicrographEPS(const MetaDataTable&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, int)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:339:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void BFactorRefiner::writePerMicrographEPS(const MetaDataTable&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, int)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:353:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void BFactorRefiner::writePerMicrographEPS(const MetaDataTable&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, int)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:355:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void BFactorRefiner::writePerMicrographEPS(const MetaDataTable&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, int)' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:359:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner_mpi.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<int, gravis::t2Vector<double> >}; _Tp = std::pair<int, gravis::t2Vector<double> >; _Alloc = std::allocator<std::pair<int, gravis::t2Vector<double> > >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<std::pair<int, gravis::t2Vector<double> > >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<int, gravis::t2Vector<double> >}; _Tp = std::pair<int, gravis::t2Vector<double> >; _Alloc = std::allocator<std::pair<int, gravis::t2Vector<double> > >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<int, gravis::t2Vector<double> >; _Alloc = std::allocator<std::pair<int, gravis::t2Vector<double> > >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN14BFactorRefiner17processMicrographElR13MetaDataTableRKSt6vectorI5ImageI8tComplexIdEESaIS6_EESA_b._omp_fn.1' at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:237:36:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, gravis::t2Vector<double> >*, std::vector<std::pair<int, gravis::t2Vector<double> > > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner_mpi.h:26,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.cpp
[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/delocalisation_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.cpp:303:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.cpp:306:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.cpp:341:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.cpp:344:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/delocalisation_helper.h:4,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/delocalisation_helper.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataPoint>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataSet>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void DefocusEstimator::writeEPS(const MetaDataTable&)' at /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.cpp:218:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void DefocusEstimator::writeEPS(const MetaDataTable&)' at /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.cpp:220:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/equation2x2.cpp
[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.cpp
[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_helper.cpp
[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/modular_ctf_optimisation.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.h:28,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/modular_ctf_optimisation.h:5,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/modular_ctf_optimisation.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.h:24:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN22MagnificationEstimator13parametricFitERSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS6_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.cpp:219:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN22MagnificationEstimator13parametricFitERSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS6_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.cpp:223:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN22MagnificationEstimator13parametricFitERSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS6_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.cpp:239:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN22MagnificationEstimator13parametricFitERSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS6_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.cpp:243:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/alignment_set.cpp
[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/frame_recombiner.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/frame_recombiner.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/frame_recombiner.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/gp_motion_fit.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/gp_motion_fit.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/gp_motion_fit.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/multidim_array.h:52,
                 from /<<PKGBUILDDIR>>/src/ctf.h:48:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  523 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void TiltHelper::extractTilt(std::vector<double, std::allocator<double> >&, double&, double&, double, double)' at /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.cpp:536:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void TiltHelper::insertTilt(std::vector<double, std::allocator<double> >&, double, double, double, double)' at /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.cpp:563:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1032 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN13TiltEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.cpp:276:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN13TiltEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.cpp:279:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN13TiltEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.cpp:310:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from '_ZN13TiltEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.cpp:313:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_helper.cpp
[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/alignment_set.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataPoint>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataSet>::iterator' changed in GCC 7.1
[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.cpp
[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner_mpi.h:27,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/three_hyperparameter_fit.cpp
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:711:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:714:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:724:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:725:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:736:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:737:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:751:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]',
    inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
    inlined from 'void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:753:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/two_hyperparameter_fit.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/alignment_set.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/three_hyperparameter_fit.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/math/Zernike.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/alignment_set.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/two_hyperparameter_fit.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/img_proc/color_helper.cpp
[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp
[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/img_proc/image_op.cpp
[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/backprojection_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/color_helper.h:5,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/color_helper.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/imod_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/backprojection_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/backprojection_helper.cpp:23:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/imod_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/imod_helper.cpp:21:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t4Matrix<double>}; _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<gravis::t4Matrix<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix<double>}; _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'static std::vector<gravis::t4Matrix<double> > ImodHelper::readTiltTransforms(std::string, gravis::d4Matrix, double, double)' at /<<PKGBUILDDIR>>/src/jaz/tomo/imod_helper.cpp:55:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gravis::t4Matrix<double>*, std::vector<gravis::t4Matrix<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/projection_helper.cpp
[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.cpp
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/projection_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/projection_helper.cpp:21:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t4Matrix<double>}; _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<gravis::t4Matrix<double> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix<double>}; _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'static std::vector<gravis::t4Matrix<double> > ProjectionHelper::loadAffineTransforms(std::string, double, double, bool)' at /<<PKGBUILDDIR>>/src/jaz/tomo/projection_helper.cpp:171:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gravis::t4Matrix<double>*, std::vector<gravis::t4Matrix<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t4Matrix<double>}; _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<gravis::t4Matrix<double> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void BackprojectionHelper::backprojectRaw(const Image<double>&, std::string, Volume<double>&, Volume<unsigned char>&, gravis::d3Vector, double, int)' at /<<PKGBUILDDIR>>/src/jaz/tomo/backprojection_helper.cpp:75:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix<double>}; _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'static void BackprojectionHelper::backprojectRaw(const Image<double>&, std::string, Volume<double>&, Volume<unsigned char>&, gravis::d3Vector, double, int)' at /<<PKGBUILDDIR>>/src/jaz/tomo/backprojection_helper.cpp:85:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gravis::t4Matrix<double>*, std::vector<gravis::t4Matrix<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static std::vector<gravis::t4Matrix<double> > ProjectionHelper::loadTiltProjectionsVol(std::string, double, double, double, double, double, double)' at /<<PKGBUILDDIR>>/src/jaz/tomo/projection_helper.cpp:105:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix<double>}; _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'static std::vector<gravis::t4Matrix<double> > ProjectionHelper::loadTiltProjectionsVol(std::string, double, double, double, double, double, double)' at /<<PKGBUILDDIR>>/src/jaz/tomo/projection_helper.cpp:115:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gravis::t4Matrix<double>*, std::vector<gravis::t4Matrix<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static std::vector<gravis::t4Matrix<double> > ProjectionHelper::loadTiltProjections(std::string, double, double)' at /<<PKGBUILDDIR>>/src/jaz/tomo/projection_helper.cpp:54:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix<double>}; _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix<double>; _Alloc = std::allocator<gravis::t4Matrix<double> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'static std::vector<gravis::t4Matrix<double> > ProjectionHelper::loadTiltProjections(std::string, double, double)' at /<<PKGBUILDDIR>>/src/jaz/tomo/projection_helper.cpp:64:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gravis::t4Matrix<double>*, std::vector<gravis::t4Matrix<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/io/star_converter.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/io/star_converter.h:5,
                 from /<<PKGBUILDDIR>>/src/jaz/io/star_converter.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsyev2.c
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsyevc3.c
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsyevd3.c
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsyevh3.c
[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsyevj3.c
[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o
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[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o
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cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/slvsec3.c
[ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /<<PKGBUILDDIR>>/src/jaz/lbfgs/lbfgs.c
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t2Vector<double>}; _Tp = gravis::t2Vector<double>; _Alloc = std::allocator<gravis::t2Vector<double> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<gravis::t2Vector<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t2Vector<double>}; _Tp = gravis::t2Vector<double>; _Alloc = std::allocator<gravis::t2Vector<double> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t2Vector<double>; _Alloc = std::allocator<gravis::t2Vector<double> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'std::vector<std::vector<gravis::t2Vector<double> > > TomoStack::loadFiducials(std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.cpp:340:28:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gravis::t2Vector<double>*, std::vector<gravis::t2Vector<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t2Vector<double>}; _Tp = gravis::t2Vector<double>; _Alloc = std::allocator<gravis::t2Vector<double> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t2Vector<double>; _Alloc = std::allocator<gravis::t2Vector<double> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'std::vector<std::vector<gravis::t2Vector<double> > > TomoStack::loadFiducials(std::string, double)' at /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.cpp:361:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gravis::t2Vector<double>*, std::vector<gravis::t2Vector<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t3Vector<double>}; _Tp = gravis::t3Vector<double>; _Alloc = std::allocator<gravis::t3Vector<double> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<gravis::t3Vector<double> >::iterator' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t3Vector<double>}; _Tp = gravis::t3Vector<double>; _Alloc = std::allocator<gravis::t3Vector<double> >]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t3Vector<double>; _Alloc = std::allocator<gravis::t3Vector<double> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'static std::vector<gravis::t3Vector<double> > FilterHelper::localMinima(Image<double>&, double)' at /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp:1683:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gravis::t3Vector<double>*, std::vector<gravis::t3Vector<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void FilterHelper::descendTV(const Image<double>&, Image<double>&, double)' at /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp:2393:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void FilterHelper::descendTV(const Image<double>&, Image<double>&, double)' at /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp:2394:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void FilterHelper::descendTV(const Image<double>&, Image<double>&, double)' at /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp:2395:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void FilterHelper::descendTV(const Image<double>&, Image<double>&, double)' at /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp:2396:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void FilterHelper::descendTV(const Image<double>&, Image<double>&, double)' at /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp:2397:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'static void FilterHelper::descendTV(const Image<double>&, Image<double>&, double)' at /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp:2398:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 53%] Linking CXX static library ../../lib/librelion_lib.a
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_lib.dir/cmake_clean_target.cmake
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 54%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /<<PKGBUILDDIR>>/src/apps/autopick.cpp
[ 54%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /<<PKGBUILDDIR>>/src/apps/align_symmetry.cpp
[ 54%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/autopick_mpi.cpp
[ 54%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /<<PKGBUILDDIR>>/src/displayer.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/autopicker.h:10,
                 from /<<PKGBUILDDIR>>/src/apps/autopick.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/align_symmetry.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/autopicker.h:10,
                 from /<<PKGBUILDDIR>>/src/autopicker_mpi.h:12,
                 from /<<PKGBUILDDIR>>/src/apps/autopick_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/displayer.h:40,
                 from /<<PKGBUILDDIR>>/src/displayer.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 54%] Linking CXX executable ../../bin/relion_autopick
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 55%] Linking CXX executable ../../bin/relion_autopick_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 55%] Built target autopick
/usr/bin/make  -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 55%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -MF CMakeFiles/convert_star.dir/convert_star.cpp.o.d -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /<<PKGBUILDDIR>>/src/apps/convert_star.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 55%] Built target autopick_mpi
[ 56%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /<<PKGBUILDDIR>>/src/gui_entries.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/io/star_converter.h:5,
                 from /<<PKGBUILDDIR>>/src/apps/convert_star.cpp:24:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 57%] Linking CXX executable ../../bin/relion_convert_star
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 57%] Built target convert_star
[ 57%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /<<PKGBUILDDIR>>/src/gui_jobwindow.cpp
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 57%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /<<PKGBUILDDIR>>/src/apps/convert_to_tiff.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/tiff_converter.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/convert_to_tiff.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 57%] Linking CXX executable ../../bin/relion_convert_to_tiff
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -o ../../bin/relion_convert_to_tiff  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 57%] Built target convert_to_tiff
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 58%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/convert_to_tiff_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/tiff_converter.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/convert_to_tiff_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 58%] Linking CXX executable ../../bin/relion_align_symmetry
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 58%] Built target align_symmetry
[ 58%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /<<PKGBUILDDIR>>/src/gui_mainwindow.cpp
[ 58%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 58%] Built target convert_to_tiff_mpi
[ 59%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /<<PKGBUILDDIR>>/src/manualpicker.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:26,
                 from /<<PKGBUILDDIR>>/src/gui_mainwindow.h:28,
                 from /<<PKGBUILDDIR>>/src/gui_mainwindow.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/manualpicker.h:43,
                 from /<<PKGBUILDDIR>>/src/manualpicker.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 59%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /<<PKGBUILDDIR>>/src/Healpix_2.15a/cxxutils.cc
/usr/bin/make  -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 59%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /<<PKGBUILDDIR>>/src/apps/ctf_mask_test.cpp
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 59%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -MF CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o.d -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /<<PKGBUILDDIR>>/src/apps/ctf_refine.cpp
[ 60%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /<<PKGBUILDDIR>>/src/Healpix_2.15a/healpix_base.cc
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/ctf_mask_test.cpp:7:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/ctf_refine.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 60%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -MF CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o.d -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/ctf_refine_mpi.cpp
[ 61%] Linking CXX executable ../../bin/relion_ctf_refine
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner_mpi.h:26,
                 from /<<PKGBUILDDIR>>/src/apps/ctf_refine_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 61%] Built target ctf_refine
/usr/bin/make  -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 62%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -MF CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o.d -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /<<PKGBUILDDIR>>/src/apps/ctf_toolbox.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/ctf_toolbox.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 62%] Linking CXX executable ../../bin/relion_ctf_refine_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 62%] Linking CXX static library ../../lib/librelion_gui_lib.a
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gui_lib.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/librelion_gui_lib.a CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o
/usr/bin/ranlib ../../lib/librelion_gui_lib.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 62%] Built target relion_gui_lib
/usr/bin/make  -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 62%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -MF CMakeFiles/demodulate.dir/demodulate.cpp.o.d -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /<<PKGBUILDDIR>>/src/apps/demodulate.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 62%] Built target ctf_refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 62%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /<<PKGBUILDDIR>>/src/apps/display.cpp
[ 63%] Linking CXX executable ../../bin/relion_ctf_mask_test
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/vtk_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/demodulate.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 63%] Built target ctf_mask_test
/usr/bin/make  -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 63%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /<<PKGBUILDDIR>>/src/apps/estimate_gain.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/display.cpp:25:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 64%] Linking CXX executable ../../bin/relion_display
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/estimate_gain.cpp:27:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 64%] Built target display
/usr/bin/make  -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 65%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -MF CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o.d -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /<<PKGBUILDDIR>>/src/apps/external_reconstruct.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/external_reconstruct.cpp:24:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 65%] Linking CXX executable ../../bin/relion_ctf_toolbox
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 65%] Built target ctf_toolbox
/usr/bin/make  -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color=
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[ 65%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -MF CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o.d -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /<<PKGBUILDDIR>>/src/apps/find_tiltpairs.cpp
[ 66%] Linking CXX executable ../../bin/relion_demodulate
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color=
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[ 66%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -MF CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o.d -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /<<PKGBUILDDIR>>/src/apps/flex_analyse.cpp
[ 66%] Linking CXX executable ../../bin/relion_estimate_gain
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -o ../../bin/relion_estimate_gain  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target estimate_gain
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 66%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -MF CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o.d -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/flex_analyse_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/exp_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/../flex_analyser.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/flex_analyse.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 66%] Linking CXX executable ../../bin/relion_external_reconstruct
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target external_reconstruct
/usr/bin/make  -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 67%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -MF CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o.d -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /<<PKGBUILDDIR>>/src/apps/helix_inimodel2d.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/exp_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/../flex_analyser.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/flex_analyse_mpi.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/../helix_inimodel2d.h:29,
                 from /<<PKGBUILDDIR>>/src/apps/helix_inimodel2d.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 68%] Linking CXX executable ../../bin/relion_find_tiltpairs
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 68%] Built target find_tiltpairs
/usr/bin/make  -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 69%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /<<PKGBUILDDIR>>/src/apps/helix_toolbox.cpp
[ 70%] Linking CXX executable ../../bin/relion_flex_analyse
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 70%] Linking CXX executable ../../bin/relion_helix_inimodel2d
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 70%] Built target helix_inimodel2d
/usr/bin/make  -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 70%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -MF CMakeFiles/image_handler.dir/image_handler.cpp.o.d -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /<<PKGBUILDDIR>>/src/apps/image_handler.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 70%] Built target flex_analyse
/usr/bin/make  -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 70%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /<<PKGBUILDDIR>>/src/apps/import.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix.h:30,
                 from /<<PKGBUILDDIR>>/src/apps/helix_toolbox.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 70%] Linking CXX executable ../../bin/relion_flex_analyse_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/image_handler.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 70%] Built target flex_analyse_mpi
/usr/bin/make  -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 71%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -MF CMakeFiles/localsym.dir/localsym.cpp.o.d -o CMakeFiles/localsym.dir/localsym.cpp.o -c /<<PKGBUILDDIR>>/src/apps/localsym.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/import.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.h:30,
                 from /<<PKGBUILDDIR>>/src/apps/localsym.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 71%] Linking CXX executable ../../bin/relion_localsym
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 71%] Built target localsym
/usr/bin/make  -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 72%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/localsym_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.h:30,
                 from /<<PKGBUILDDIR>>/src/local_symmetry_mpi.h:5,
                 from /<<PKGBUILDDIR>>/src/apps/localsym_mpi.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 72%] Linking CXX executable ../../bin/relion_import
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 72%] Linking CXX executable ../../bin/relion_localsym_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 72%] Built target import
/usr/bin/make  -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 72%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /<<PKGBUILDDIR>>/src/apps/maingui.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 72%] Built target localsym_mpi
/usr/bin/make  -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 72%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -MF CMakeFiles/manualpick.dir/manualpick.cpp.o.d -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /<<PKGBUILDDIR>>/src/apps/manualpick.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/manualpick.cpp:25:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:26,
                 from /<<PKGBUILDDIR>>/src/gui_mainwindow.h:28,
                 from /<<PKGBUILDDIR>>/src/apps/maingui.cpp:23:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 73%] Linking CXX executable ../../bin/relion_manualpick
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff 
[ 74%] Linking CXX executable ../../bin/relion
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/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/relion.dir/maingui.cpp.o -o ../../bin/relion  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff 
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cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 75%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /<<PKGBUILDDIR>>/src/apps/merge_particles.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/mask_create.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/io/star_converter.h:5,
                 from /<<PKGBUILDDIR>>/src/apps/merge_particles.cpp:2:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 75%] Linking CXX executable ../../bin/relion_merge_particles
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/merge_particles.dir/merge_particles.cpp.o -o ../../bin/relion_merge_particles  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 75%] Built target merge_particles
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 76%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -MF CMakeFiles/motion_refine.dir/motion_refine.cpp.o.d -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /<<PKGBUILDDIR>>/src/apps/motion_refine.cpp
[ 76%] Linking CXX executable ../../bin/relion_helix_toolbox
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/motion_refine.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 76%] Built target helix_toolbox
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 76%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/motion_refine_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner_mpi.h:27,
                 from /<<PKGBUILDDIR>>/src/apps/motion_refine_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 77%] Linking CXX executable ../../bin/relion_image_handler
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 77%] Linking CXX executable ../../bin/relion_motion_refine
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 77%] Built target image_handler
/usr/bin/make  -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 77%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -MF CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o.d -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /<<PKGBUILDDIR>>/src/apps/mrc2vtk.cpp
[ 77%] Linking CXX executable ../../bin/relion_mask_create
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 77%] Built target mask_create
/usr/bin/make  -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 78%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_FCC.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 78%] Built target motion_refine
/usr/bin/make  -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 79%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -MF CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o.d -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_reposition.cpp
[ 80%] Linking CXX executable ../../bin/relion_motion_refine_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/mrc2vtk.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/particle_FCC.cpp:7:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/apps/particle_reposition.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 80%] Built target motion_refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 80%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_select.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/stack_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/particle_select.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 80%] Linking CXX executable ../../bin/relion_particle_FCC
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 80%] Built target particle_FCC
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 80%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -MF CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o.d -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_subtract.cpp
[ 80%] Linking CXX executable ../../bin/relion_mrc2vtk
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 80%] Built target mrc2vtk
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 80%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -MF CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o.d -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_subtract_mpi.cpp
[ 81%] Linking CXX executable ../../bin/relion_particle_select
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_select.dir/particle_select.cpp.o -o ../../bin/relion_particle_select  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/apps/../particle_subtractor.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/particle_subtract.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 81%] Built target particle_select
/usr/bin/make  -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 82%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_symmetry_expand.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/apps/../particle_subtractor.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/particle_subtract_mpi.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/particle_symmetry_expand.cpp:26:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 82%] Linking CXX executable ../../bin/relion_particle_symmetry_expand
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -o ../../bin/relion_particle_symmetry_expand  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target particle_symmetry_expand
/usr/bin/make  -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 82%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o -MF CMakeFiles/pipeliner.dir/pipeliner.cpp.o.d -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /<<PKGBUILDDIR>>/src/apps/pipeliner.cpp
[ 83%] Linking CXX executable ../../bin/relion_particle_subtract
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target particle_subtract
/usr/bin/make  -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 83%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -MF CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o.d -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /<<PKGBUILDDIR>>/src/apps/plot_delocalisation.cpp
[ 83%] Linking CXX executable ../../bin/relion_particle_subtract_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/plot_delocalisation.cpp:7:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target particle_subtract_mpi
/usr/bin/make  -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 83%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /<<PKGBUILDDIR>>/src/apps/postprocess.cpp
[ 84%] Linking CXX executable ../../bin/relion_pipeliner
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/args.h:52,
                 from /<<PKGBUILDDIR>>/src/apps/plot_delocalisation.cpp:6:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataPoint>::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<CDataSet>::iterator' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 84%] Built target pipeliner
/usr/bin/make  -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 85%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/postprocess_mpi.cpp
[ 85%] Linking CXX executable ../../bin/relion_particle_reposition
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/postprocessing.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/postprocess.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'int main(int, char**)' at /<<PKGBUILDDIR>>/src/apps/plot_delocalisation.cpp:207:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]',
    inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
    inlined from 'int main(int, char**)' at /<<PKGBUILDDIR>>/src/apps/plot_delocalisation.cpp:213:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target particle_reposition
/usr/bin/make  -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 85%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp
[ 86%] Linking CXX executable ../../bin/relion_plot_delocalisation
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/postprocessing.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/postprocess_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 86%] Linking CXX executable ../../bin/relion_postprocess
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 86%] Built target postprocess
/usr/bin/make  -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 86%] Built target plot_delocalisation
/usr/bin/make  -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color=
[ 86%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /<<PKGBUILDDIR>>/src/apps/preprocess.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 86%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/preprocess_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix.h:30,
                 from /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 86%] Linking CXX executable ../../bin/relion_postprocess_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
                 from /<<PKGBUILDDIR>>/src/apps/preprocess.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 86%] Built target postprocess_mpi
/usr/bin/make  -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 87%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /<<PKGBUILDDIR>>/src/apps/project.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
                 from /<<PKGBUILDDIR>>/src/preprocessing_mpi.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/preprocess_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 88%] Linking CXX executable ../../bin/relion_preprocess
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 88%] Linking CXX executable ../../bin/relion_preprocess_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/project.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] Built target preprocess
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 88%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /<<PKGBUILDDIR>>/src/apps/reconstruct.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] Built target preprocess_mpi
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 88%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/reconstruct_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/reconstructor.h:23,
                 from /<<PKGBUILDDIR>>/src/apps/reconstruct.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/reconstructor.h:23,
                 from /<<PKGBUILDDIR>>/src/reconstructor_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/reconstruct_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/args.h:52,
                 from /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp:21:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
[ 89%] Linking CXX executable ../../bin/relion_reconstruct
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 90%] Linking CXX executable ../../bin/relion_reconstruct_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 90%] Built target reconstruct
/usr/bin/make  -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 90%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /<<PKGBUILDDIR>>/src/apps/refine.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 90%] Built target reconstruct_mpi
/usr/bin/make  -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 91%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/refine_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/apps/refine.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/refine_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void prepare_subtomo::run()' at /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp:634:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void prepare_subtomo::run()' at /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp:652:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void prepare_subtomo::run()' at /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp:801:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void prepare_subtomo::run()' at /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp:802:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void prepare_subtomo::run()' at /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp:816:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
    inlined from 'void prepare_subtomo::run()' at /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp:833:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 91%] Linking CXX executable ../../bin/relion_refine
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 91%] Linking CXX executable ../../bin/relion_refine_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target refine
/usr/bin/make  -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color=
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/usr/bin/make  -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build
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[ 91%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /<<PKGBUILDDIR>>/src/apps/reposition.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Linking CXX executable ../../bin/relion_project
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1
[ 91%] Built target refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 91%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /<<PKGBUILDDIR>>/src/apps/run_ctffind.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target project
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/reposition.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 92%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/run_ctffind_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.h:31,
                 from /<<PKGBUILDDIR>>/src/apps/run_ctffind.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.h:31,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/run_ctffind_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 92%] Linking CXX executable ../../bin/relion_run_ctffind
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 92%] Built target run_ctffind
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 93%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /<<PKGBUILDDIR>>/src/apps/run_motioncorr.cpp
[ 93%] Linking CXX executable ../../bin/relion_run_ctffind_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 93%] Built target run_ctffind_mpi
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 93%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -MF CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o.d -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/run_motioncorr_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.h:32,
                 from /<<PKGBUILDDIR>>/src/apps/run_motioncorr.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.h:32,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/run_motioncorr_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 94%] Linking CXX executable ../../bin/relion_reposition
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 95%] Linking CXX executable ../../bin/relion_prepare_subtomo
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -o ../../bin/relion_prepare_subtomo  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 95%] Linking CXX executable ../../bin/relion_run_motioncorr
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 95%] Built target reposition
/usr/bin/make  -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 95%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /<<PKGBUILDDIR>>/src/apps/scheduler.cpp
[ 95%] Built target prepare_subtomo
/usr/bin/make  -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 96%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /<<PKGBUILDDIR>>/src/apps/stack_create.cpp
[ 97%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 97%] Built target run_motioncorr
/usr/bin/make  -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 98%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /<<PKGBUILDDIR>>/src/apps/star_handler.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 98%] Built target run_motioncorr_mpi
/usr/bin/make  -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 98%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /<<PKGBUILDDIR>>/src/apps/tiltpair_plot.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:26,
                 from /<<PKGBUILDDIR>>/src/apps/scheduler.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/stack_create.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/star_handler.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/tiltpair_plot.cpp:25:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 99%] Linking CXX executable ../../bin/relion_tiltpair_plot
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -o ../../bin/relion_tiltpair_plot  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 99%] Built target tiltpair_plot
/usr/bin/make  -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 99%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -MF CMakeFiles/tomo_test.dir/tomo_test.cpp.o.d -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /<<PKGBUILDDIR>>/src/apps/tomo_test.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/tomo_test.cpp:2:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function 'int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)':
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:84:38: note: declared here
   84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:81:38: note: declared here
   81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 99%] Linking CXX executable ../../bin/relion_scheduler
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 99%] Built target scheduler
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gravis::t3Vector<double>&}; _Tp = gravis::t3Vector<double>; _Alloc = std::allocator<gravis::t3Vector<double> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<gravis::t3Vector<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/src/funcs.h:56,
                 from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
[ 99%] Linking CXX executable ../../bin/relion_stack_create
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 99%] Built target stack_create
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gravis::t3Vector<double>; _Alloc = std::allocator<gravis::t3Vector<double> >]',
    inlined from 'int main(int, char**)' at /<<PKGBUILDDIR>>/src/apps/tomo_test.cpp:107:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gravis::t3Vector<double>*, std::vector<gravis::t3Vector<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[100%] Linking CXX executable ../../bin/relion_tomo_test
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void star_handler_parameters::discard_on_image_stats()' at /<<PKGBUILDDIR>>/src/apps/star_handler.cpp:292:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void star_handler_parameters::discard_on_image_stats()' at /<<PKGBUILDDIR>>/src/apps/star_handler.cpp:293:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target tomo_test
[100%] Linking CXX executable ../../bin/relion_star_handler
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/star_handler.dir/star_handler.cpp.o -o ../../bin/relion_star_handler  ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target star_handler
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
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make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -C build install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp/cli
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/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles /<<PKGBUILDDIR>>/build//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_printtable /<<PKGBUILDDIR>>/build/bin/relion_star_printtable
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_plottable /<<PKGBUILDDIR>>/build/bin/relion_star_plottable
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_loopheader /<<PKGBUILDDIR>>/build/bin/relion_star_loopheader
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_stack /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_stack
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_singlefiles /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_singlefiles
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_ctfdat /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_ctfdat
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/qsub.csh /<<PKGBUILDDIR>>/build/bin/relion_qsub.csh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[  0%] Built target copy_scripts
/usr/bin/make  -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_lib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 53%] Built target relion_lib
/usr/bin/make  -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_gui_lib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 56%] Built target relion_gui_lib
/usr/bin/make  -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/align_symmetry.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 56%] Built target align_symmetry
/usr/bin/make  -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 57%] Built target autopick
/usr/bin/make  -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 58%] Built target autopick_mpi
/usr/bin/make  -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_star.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 59%] Built target convert_star
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 59%] Built target convert_to_tiff
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 60%] Built target convert_to_tiff_mpi
/usr/bin/make  -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_mask_test.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 61%] Built target ctf_mask_test
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 62%] Built target ctf_refine
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 62%] Built target ctf_refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_toolbox.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 63%] Built target ctf_toolbox
/usr/bin/make  -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/demodulate.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 64%] Built target demodulate
/usr/bin/make  -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/display.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 65%] Built target display
/usr/bin/make  -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/estimate_gain.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 65%] Built target estimate_gain
/usr/bin/make  -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/external_reconstruct.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target external_reconstruct
/usr/bin/make  -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/find_tiltpairs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 67%] Built target find_tiltpairs
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 68%] Built target flex_analyse
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 68%] Built target flex_analyse_mpi
/usr/bin/make  -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_inimodel2d.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 69%] Built target helix_inimodel2d
/usr/bin/make  -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_toolbox.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 70%] Built target helix_toolbox
/usr/bin/make  -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/image_handler.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 71%] Built target image_handler
/usr/bin/make  -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/import.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 71%] Built target import
/usr/bin/make  -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 72%] Built target localsym
/usr/bin/make  -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 73%] Built target localsym_mpi
/usr/bin/make  -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 74%] Built target relion
/usr/bin/make  -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/manualpick.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 75%] Built target manualpick
/usr/bin/make  -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/mask_create.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 75%] Built target mask_create
/usr/bin/make  -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/merge_particles.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 76%] Built target merge_particles
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 77%] Built target motion_refine
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 78%] Built target motion_refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/mrc2vtk.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 78%] Built target mrc2vtk
/usr/bin/make  -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_FCC.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 79%] Built target particle_FCC
/usr/bin/make  -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_reposition.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 80%] Built target particle_reposition
/usr/bin/make  -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_select.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 81%] Built target particle_select
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target particle_subtract
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target particle_subtract_mpi
/usr/bin/make  -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_symmetry_expand.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target particle_symmetry_expand
/usr/bin/make  -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/pipeliner.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 84%] Built target pipeliner
/usr/bin/make  -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/plot_delocalisation.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target plot_delocalisation
/usr/bin/make  -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target postprocess
/usr/bin/make  -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 86%] Built target postprocess_mpi
/usr/bin/make  -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/prepare_subtomo.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 87%] Built target prepare_subtomo
/usr/bin/make  -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] Built target preprocess
/usr/bin/make  -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] Built target preprocess_mpi
/usr/bin/make  -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/project.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 89%] Built target project
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 90%] Built target reconstruct
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color=
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/usr/bin/make  -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target reconstruct_mpi
/usr/bin/make  -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine.dir/build'.
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[ 91%] Built target refine
/usr/bin/make  -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine_mpi.dir/build'.
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[ 92%] Built target refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
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[ 93%] Built target reposition
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind.dir/build'.
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[ 93%] Built target run_ctffind
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind_mpi.dir/build'.
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[ 94%] Built target run_ctffind_mpi
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr.dir/build'.
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[ 95%] Built target run_motioncorr
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color=
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/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 96%] Built target run_motioncorr_mpi
/usr/bin/make  -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color=
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/usr/bin/make  -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/scheduler.dir/build'.
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[ 96%] Built target scheduler
/usr/bin/make  -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color=
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/usr/bin/make  -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/stack_create.dir/build'.
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[ 97%] Built target stack_create
/usr/bin/make  -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color=
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/usr/bin/make  -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build
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make[4]: Nothing to be done for 'src/apps/CMakeFiles/star_handler.dir/build'.
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[ 98%] Built target star_handler
/usr/bin/make  -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color=
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/usr/bin/make  -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/tiltpair_plot.dir/build'.
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[ 99%] Built target tiltpair_plot
/usr/bin/make  -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/tomo_test.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target tomo_test
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
make[3]: Nothing to be done for 'preinstall'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_star
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_align_symmetry
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_refine
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_mask_test
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_display
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_toolbox
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_demodulate
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_estimate_gain
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_external_reconstruct
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_find_tiltpairs
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_import
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_manualpick
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_merge_particles
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_toolbox
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_image_handler
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mask_create
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_FCC
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mrc2vtk
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_select
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_pipeliner
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_reposition
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_plot_delocalisation
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_preprocess
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_preprocess_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reconstruct
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_refine
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_refine_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_project
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_ctffind
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reposition
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_prepare_subtomo
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_motioncorr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_tiltpair_plot
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_scheduler
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_stack_create
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_tomo_test
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_handler
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_printtable
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_plottable
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_loopheader
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_datablock_stack
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_qsub.csh
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_align_symmetry
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_star
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_mask_test
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_refine
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_toolbox
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_demodulate
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_display
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_estimate_gain
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_external_reconstruct
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_find_tiltpairs
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_toolbox
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_image_handler
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_import
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_manualpick
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mask_create
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_merge_particles
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mrc2vtk
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_FCC
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_reposition
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_select
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_pipeliner
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_plot_delocalisation
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_prepare_subtomo
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_preprocess
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_preprocess_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_project
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reconstruct
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_refine
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_refine_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reposition
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_ctffind
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_motioncorr
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_scheduler
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_stack_create
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_handler
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_tiltpair_plot
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_tomo_test
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
mkdir -p /<<PKGBUILDDIR>>/debian/tmp/gui/usr/bin
rm /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/*.csh # Useless ...
set -e; for prog in relion relion_display relion_manualpick; do \
  mv /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/$prog \
    /<<PKGBUILDDIR>>/debian/tmp/gui/usr/bin; done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -a
   dh_installdocs -a
   dh_installchangelogs -a
   dh_lintian -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reconstruct contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_tomo_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion_display contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_preprocess_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion_manualpick contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_autopick_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/relion-gui/usr/bin/relion_display debian/relion-gui/usr/bin/relion_manualpick debian/relion-gui/usr/bin/relion were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_motioncorr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_FCC contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_flex_analyse contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_merge_particles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_postprocess_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_ctffind contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_reposition contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_helix_toolbox contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_star_handler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_demodulate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_plot_delocalisation contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_project contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_motion_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_tiltpair_plot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_estimate_gain contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_image_handler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_helix_inimodel2d contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_select contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_preprocess contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_find_tiltpairs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_autopick contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_mrc2vtk contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_scheduler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_to_tiff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_flex_analyse_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_localsym contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_pipeliner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_motioncorr_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_import contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_ctffind_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_mask_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reposition contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_motion_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_star contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_subtract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_toolbox contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_stack_create contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_localsym_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_prepare_subtomo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_external_reconstruct contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reconstruct_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_symmetry_expand contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_subtract_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_postprocess contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_mask_create contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_align_symmetry contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_to_tiff_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/relion/usr/bin/relion_reconstruct debian/relion/usr/bin/relion_tomo_test debian/relion/usr/bin/relion_preprocess_mpi debian/relion/usr/bin/relion_autopick_mpi debian/relion/usr/bin/relion_run_motioncorr debian/relion/usr/bin/relion_particle_FCC debian/relion/usr/bin/relion_flex_analyse debian/relion/usr/bin/relion_merge_particles debian/relion/usr/bin/relion_postprocess_mpi debian/relion/usr/bin/relion_run_ctffind debian/relion/usr/bin/relion_particle_reposition debian/relion/usr/bin/relion_helix_toolbox debian/relion/usr/bin/relion_star_handler debian/relion/usr/bin/relion_demodulate debian/relion/usr/bin/relion_plot_delocalisation debian/relion/usr/bin/relion_project debian/relion/usr/bin/relion_motion_refine debian/relion/usr/bin/relion_tiltpair_plot debian/relion/usr/bin/relion_estimate_gain debian/relion/usr/bin/relion_image_handler debian/relion/usr/bin/relion_helix_inimodel2d debian/relion/usr/bin/relion_particle_select debian/relion/usr/bin/relion_preprocess debian/relion/usr/bin/relion_find_tiltpairs debian/relion/usr/bin/relion_autopick debian/relion/usr/bin/relion_mrc2vtk debian/relion/usr/bin/relion_scheduler debian/relion/usr/bin/relion_convert_to_tiff debian/relion/usr/bin/relion_ctf_refine debian/relion/usr/bin/relion_refine debian/relion/usr/bin/relion_flex_analyse_mpi debian/relion/usr/bin/relion_localsym debian/relion/usr/bin/relion_refine_mpi debian/relion/usr/bin/relion_pipeliner debian/relion/usr/bin/relion_run_motioncorr_mpi debian/relion/usr/bin/relion_import debian/relion/usr/bin/relion_run_ctffind_mpi debian/relion/usr/bin/relion_ctf_mask_test debian/relion/usr/bin/relion_reposition debian/relion/usr/bin/relion_motion_refine_mpi debian/relion/usr/bin/relion_convert_star debian/relion/usr/bin/relion_particle_subtract debian/relion/usr/bin/relion_ctf_toolbox debian/relion/usr/bin/relion_stack_create debian/relion/usr/bin/relion_localsym_mpi debian/relion/usr/bin/relion_prepare_subtomo debian/relion/usr/bin/relion_external_reconstruct debian/relion/usr/bin/relion_reconstruct_mpi debian/relion/usr/bin/relion_particle_symmetry_expand debian/relion/usr/bin/relion_particle_subtract_mpi debian/relion/usr/bin/relion_postprocess debian/relion/usr/bin/relion_mask_create debian/relion/usr/bin/relion_align_symmetry debian/relion/usr/bin/relion_convert_to_tiff_mpi debian/relion/usr/bin/relion_ctf_refine_mpi were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'relion' in '../relion_3.1.3-3_armhf.deb'.
dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.3-3_armhf.deb'.
dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.3-3_armhf.deb'.
dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3_armhf.deb'.
 dpkg-genbuildinfo --build=any -O../relion_3.1.3-3_armhf.buildinfo
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../relion_3.1.3-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-12-11T09:58:37Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


relion_3.1.3-3_armhf.changes:
-----------------------------

Format: 1.8
Date: Tue, 06 Dec 2022 11:56:43 +0100
Source: relion
Binary: relion relion-dbgsym relion-gui relion-gui-dbgsym
Architecture: armhf
Version: 3.1.3-3
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 relion     - toolkit for 3D reconstructions in cryo-electron microscopy
 relion-gui - toolkit for 3D reconstructions in cryo-electron microscopy (gui a
Changes:
 relion (3.1.3-3) unstable; urgency=medium
 .
   * Fix watch file
Checksums-Sha1:
 93b4e10635c8273df0a33b9031ff22cbb3005feb 329842404 relion-dbgsym_3.1.3-3_armhf.deb
 0c0069a59788cb57ae3e3457ab2d7ede6b4db123 19951216 relion-gui-dbgsym_3.1.3-3_armhf.deb
 54388249a76c51f10d8eef492f3d2af81cf40679 851960 relion-gui_3.1.3-3_armhf.deb
 77e0734254ba4cc8b5c38296a80325df4fad9064 9944 relion_3.1.3-3_armhf.buildinfo
 36097a69fb5b12d60b35c17d43e0e18bc0aa74ce 9355024 relion_3.1.3-3_armhf.deb
Checksums-Sha256:
 3e8e97bba1d2313c2b434a5b4ca0bf5f2abe97fdd0bd7ccb468b64720d71b12e 329842404 relion-dbgsym_3.1.3-3_armhf.deb
 e4f15b5c01744c1b63180e6873a741e4c89531ec697ac6f067cdabc6def99df1 19951216 relion-gui-dbgsym_3.1.3-3_armhf.deb
 bae35b5109d4ca1cf64c0fb709f7b57fcd294751742dc7856f595100ea62cb02 851960 relion-gui_3.1.3-3_armhf.deb
 0d64786ff6f58f4155a589d8a366c271b048236caf05f16466a38a036e2f4e58 9944 relion_3.1.3-3_armhf.buildinfo
 30e231d95d74f9e589f0aa261e6e7e9a1a0b5acbcf1f0e26492c3dcfda921a24 9355024 relion_3.1.3-3_armhf.deb
Files:
 ac2d152097a1fb2f59cd371c61bc9773 329842404 debug optional relion-dbgsym_3.1.3-3_armhf.deb
 68c08d282ff98365cfbf1f047ce8aed6 19951216 debug optional relion-gui-dbgsym_3.1.3-3_armhf.deb
 949afada64dad36baeadf3277d8d166d 851960 science optional relion-gui_3.1.3-3_armhf.deb
 aaea08387c5f02d4883861d705a5b2fc 9944 science optional relion_3.1.3-3_armhf.buildinfo
 f4e92c30f73884e28d3a8b6f1db84106 9355024 science optional relion_3.1.3-3_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


relion-dbgsym_3.1.3-3_armhf.deb
-------------------------------

 new Debian package, version 2.0.
 size 329842404 bytes: control archive=3076 bytes.
    2583 bytes,    12 lines      control              
    5916 bytes,    56 lines      md5sums              
 Package: relion-dbgsym
 Source: relion
 Version: 3.1.3-3
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 339143
 Depends: relion (= 3.1.3-3)
 Section: debug
 Priority: optional
 Description: debug symbols for relion
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drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root   5748552 2022-12-06 10:56 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/relion.debug
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/doc/
lrwxrwxrwx root/root         0 2022-12-06 10:56 ./usr/share/doc/relion-dbgsym -> relion


relion-gui-dbgsym_3.1.3-3_armhf.deb
-----------------------------------

 new Debian package, version 2.0.
 size 19951216 bytes: control archive=700 bytes.
     462 bytes,    12 lines      control              
     408 bytes,     4 lines      md5sums              
 Package: relion-gui-dbgsym
 Source: relion
 Version: 3.1.3-3
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 20479
 Depends: relion-gui (= 3.1.3-3)
 Section: debug
 Priority: optional
 Description: debug symbols for relion-gui
 Build-Ids: 25ff6eb57151a13a77aa58165022bb8852caaa61 99aeeda6b9dcb2e9bb5102687e295323cc1cf96c d10353b53c41458e689695d32e05722b716990c3

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drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/debug/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/debug/.build-id/25/
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drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/debug/.build-id/99/
-rw-r--r-- root/root  10905916 2022-12-06 10:56 ./usr/lib/debug/.build-id/99/aeeda6b9dcb2e9bb5102687e295323cc1cf96c.debug
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/debug/.build-id/d1/
-rw-r--r-- root/root   4219816 2022-12-06 10:56 ./usr/lib/debug/.build-id/d1/0353b53c41458e689695d32e05722b716990c3.debug
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root   1010328 2022-12-06 10:56 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/relion-gui.debug
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/doc/
lrwxrwxrwx root/root         0 2022-12-06 10:56 ./usr/share/doc/relion-gui-dbgsym -> relion-gui


relion-gui_3.1.3-3_armhf.deb
----------------------------

 new Debian package, version 2.0.
 size 851960 bytes: control archive=1084 bytes.
    1126 bytes,    22 lines      control              
     387 bytes,     6 lines      md5sums              
 Package: relion-gui
 Source: relion
 Version: 3.1.3-3
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4318
 Depends: relion (= 3.1.3-3), libc6 (>= 2.34), libfftw3-double3 (>= 3.3.10), libfltk1.3 (>= 1.3.4), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libstdc++6 (>= 11), libtiff5 (>= 4.0.3)
 Conflicts: relion-cuda-gui
 Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui
 Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui
 Section: science
 Priority: optional
 Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
 Description: toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
  RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
  computer program for Maximum A Posteriori refinement of (multiple) 3D
  reconstructions or 2D class averages in cryo-electron microscopy.
  .
  RELION provides a GUI, several command-line tools in parallel (MPI) and serial
  versions, optionally with CUDA/GPU support.
  .
  relion-gui provides the graphical user interface without CUDA/GPU support.

drwxr-xr-x root/root         0 2022-12-06 10:56 ./
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/bin/
-rwxr-xr-x root/root   2365228 2022-12-06 10:56 ./usr/bin/relion
-rwxr-xr-x root/root   1115920 2022-12-06 10:56 ./usr/bin/relion_display
-rwxr-xr-x root/root    919312 2022-12-06 10:56 ./usr/bin/relion_manualpick
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/doc/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/doc/relion-gui/
-rw-r--r-- root/root      1086 2022-12-06 10:56 ./usr/share/doc/relion-gui/changelog.Debian.gz
-rw-r--r-- root/root      7408 2022-12-06 10:56 ./usr/share/doc/relion-gui/copyright
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/lintian/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/lintian/overrides/
-rw-r--r-- root/root        15 2022-12-06 10:56 ./usr/share/lintian/overrides/relion-gui


relion_3.1.3-3_armhf.deb
------------------------

 new Debian package, version 2.0.
 size 9355024 bytes: control archive=2644 bytes.
    1148 bytes,    22 lines      control              
    4218 bytes,    66 lines      md5sums              
 Package: relion
 Version: 3.1.3-3
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 75409
 Depends: openmpi-gcc | openmpi-bin, libc6 (>= 2.34), libfftw3-double3 (>= 3.3.10), libfftw3-single3 (>= 3.3.10), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libopenmpi3 (>= 4.1.4), libstdc++6 (>= 11), libtiff5 (>= 4.0.3)
 Conflicts: relion-cuda
 Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui
 Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui
 Section: science
 Priority: optional
 Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
 Description: toolkit for 3D reconstructions in cryo-electron microscopy
  RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
  computer program for Maximum A Posteriori refinement of (multiple) 3D
  reconstructions or 2D class averages in cryo-electron microscopy.
  .
  RELION provides a GUI, several command-line tools in parallel (MPI) and serial
  versions, optionally with CUDA/GPU support.
  .
  relion provides the serial and parallel (MPI) command-line tools without
  CUDA/GPU support.

drwxr-xr-x root/root         0 2022-12-06 10:56 ./
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/bin/
-rwxr-xr-x root/root    788232 2022-12-06 10:56 ./usr/bin/relion_align_symmetry
-rwxr-xr-x root/root   1705736 2022-12-06 10:56 ./usr/bin/relion_autopick
-rwxr-xr-x root/root   1705736 2022-12-06 10:56 ./usr/bin/relion_autopick_mpi
-rwxr-xr-x root/root   1246984 2022-12-06 10:56 ./usr/bin/relion_convert_star
-rwxr-xr-x root/root    919308 2022-12-06 10:56 ./usr/bin/relion_convert_to_tiff
-rwxr-xr-x root/root    919308 2022-12-06 10:56 ./usr/bin/relion_convert_to_tiff_mpi
-rwxr-xr-x root/root   1378060 2022-12-06 10:56 ./usr/bin/relion_ctf_mask_test
-rwxr-xr-x root/root   1967888 2022-12-06 10:56 ./usr/bin/relion_ctf_refine
-rwxr-xr-x root/root   1967888 2022-12-06 10:56 ./usr/bin/relion_ctf_refine_mpi
-rwxr-xr-x root/root    919304 2022-12-06 10:56 ./usr/bin/relion_ctf_toolbox
-rwxr-xr-x root/root   1312520 2022-12-06 10:56 ./usr/bin/relion_demodulate
-rwxr-xr-x root/root    722696 2022-12-06 10:56 ./usr/bin/relion_estimate_gain
-rwxr-xr-x root/root    919304 2022-12-06 10:56 ./usr/bin/relion_external_reconstruct
-rwxr-xr-x root/root    526088 2022-12-06 10:56 ./usr/bin/relion_find_tiltpairs
-rwxr-xr-x root/root   1967880 2022-12-06 10:56 ./usr/bin/relion_flex_analyse
-rwxr-xr-x root/root   1967880 2022-12-06 10:56 ./usr/bin/relion_flex_analyse_mpi
-rwxr-xr-x root/root    984840 2022-12-06 10:56 ./usr/bin/relion_helix_inimodel2d
-rwxr-xr-x root/root   1312520 2022-12-06 10:56 ./usr/bin/relion_helix_toolbox
-rwxr-xr-x root/root   1050376 2022-12-06 10:56 ./usr/bin/relion_image_handler
-rwxr-xr-x root/root    919304 2022-12-06 10:56 ./usr/bin/relion_import
-rwxr-xr-x root/root   1640200 2022-12-06 10:56 ./usr/bin/relion_localsym
-rwxr-xr-x root/root   1705736 2022-12-06 10:56 ./usr/bin/relion_localsym_mpi
-rwxr-xr-x root/root   1312520 2022-12-06 10:56 ./usr/bin/relion_mask_create
-rwxr-xr-x root/root    853772 2022-12-06 10:56 ./usr/bin/relion_merge_particles
-rwxr-xr-x root/root   2361120 2022-12-06 10:56 ./usr/bin/relion_motion_refine
-rwxr-xr-x root/root   2361120 2022-12-06 10:56 ./usr/bin/relion_motion_refine_mpi
-rwxr-xr-x root/root    657160 2022-12-06 10:56 ./usr/bin/relion_mrc2vtk
-rwxr-xr-x root/root   1574668 2022-12-06 10:56 ./usr/bin/relion_particle_FCC
-rwxr-xr-x root/root   2492168 2022-12-06 10:56 ./usr/bin/relion_particle_reposition
-rwxr-xr-x root/root   1246988 2022-12-06 10:56 ./usr/bin/relion_particle_select
-rwxr-xr-x root/root   2492172 2022-12-06 10:56 ./usr/bin/relion_particle_subtract
-rwxr-xr-x root/root   2492168 2022-12-06 10:56 ./usr/bin/relion_particle_subtract_mpi
-rwxr-xr-x root/root    984844 2022-12-06 10:56 ./usr/bin/relion_particle_symmetry_expand
-rwxr-xr-x root/root   1246984 2022-12-06 10:56 ./usr/bin/relion_pipeliner
-rwxr-xr-x root/root   1246984 2022-12-06 10:56 ./usr/bin/relion_plot_delocalisation
-rwxr-xr-x root/root    788236 2022-12-06 10:56 ./usr/bin/relion_postprocess
-rwxr-xr-x root/root    788236 2022-12-06 10:56 ./usr/bin/relion_postprocess_mpi
-rwxr-xr-x root/root    722696 2022-12-06 10:56 ./usr/bin/relion_prepare_subtomo
-rwxr-xr-x root/root   1312524 2022-12-06 10:56 ./usr/bin/relion_preprocess
-rwxr-xr-x root/root   1378060 2022-12-06 10:56 ./usr/bin/relion_preprocess_mpi
-rwxr-xr-x root/root   1902344 2022-12-06 10:56 ./usr/bin/relion_project
-rwxr-xr-x root/root   1902348 2022-12-06 10:56 ./usr/bin/relion_reconstruct
-rwxr-xr-x root/root   1967884 2022-12-06 10:56 ./usr/bin/relion_reconstruct_mpi
-rwxr-xr-x root/root   2426632 2022-12-06 10:56 ./usr/bin/relion_refine
-rwxr-xr-x root/root   2557704 2022-12-06 10:56 ./usr/bin/relion_refine_mpi
-rwxr-xr-x root/root   1574664 2022-12-06 10:56 ./usr/bin/relion_reposition
-rwxr-xr-x root/root    984840 2022-12-06 10:56 ./usr/bin/relion_run_ctffind
-rwxr-xr-x root/root    984840 2022-12-06 10:56 ./usr/bin/relion_run_ctffind_mpi
-rwxr-xr-x root/root   1246984 2022-12-06 10:56 ./usr/bin/relion_run_motioncorr
-rwxr-xr-x root/root   1246984 2022-12-06 10:56 ./usr/bin/relion_run_motioncorr_mpi
-rwxr-xr-x root/root   1771272 2022-12-06 10:56 ./usr/bin/relion_scheduler
-rwxr-xr-x root/root    919304 2022-12-06 10:56 ./usr/bin/relion_stack_create
-rwxr-xr-x root/root      1055 2022-12-06 10:56 ./usr/bin/relion_star_datablock_ctfdat
-rwxr-xr-x root/root       714 2022-12-06 10:56 ./usr/bin/relion_star_datablock_singlefiles
-rwxr-xr-x root/root       767 2022-12-06 10:56 ./usr/bin/relion_star_datablock_stack
-rwxr-xr-x root/root    984840 2022-12-06 10:56 ./usr/bin/relion_star_handler
-rwxr-xr-x root/root       675 2022-12-06 10:56 ./usr/bin/relion_star_loopheader
-rwxr-xr-x root/root      1217 2022-12-06 10:56 ./usr/bin/relion_star_plottable
-rwxr-xr-x root/root      2263 2022-12-06 10:56 ./usr/bin/relion_star_printtable
-rwxr-xr-x root/root    591624 2022-12-06 10:56 ./usr/bin/relion_tiltpair_plot
-rwxr-xr-x root/root   1246984 2022-12-06 10:56 ./usr/bin/relion_tomo_test
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/doc/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/doc/relion/
-rw-r--r-- root/root      1433 2021-08-31 10:17 ./usr/share/doc/relion/AUTHORS
-rw-r--r-- root/root      2810 2021-08-31 10:17 ./usr/share/doc/relion/README.md.gz
-rw-r--r-- root/root      1086 2022-12-06 10:56 ./usr/share/doc/relion/changelog.Debian.gz
-rw-r--r-- root/root      7408 2022-12-06 10:56 ./usr/share/doc/relion/copyright
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/lintian/
drwxr-xr-x root/root         0 2022-12-06 10:56 ./usr/share/lintian/overrides/
-rw-r--r-- root/root        15 2022-12-06 10:56 ./usr/share/lintian/overrides/relion


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 4062520
Build-Time: 7013
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 1446
Job: relion_3.1.3-3
Machine Architecture: armhf
Package: relion
Package-Time: 8518
Source-Version: 3.1.3-3
Space: 4062520
Status: successful
Version: 3.1.3-3
--------------------------------------------------------------------------------
Finished at 2022-12-11T09:58:37Z
Build needed 02:21:58, 4062520k disc space
Raspbian Package Auto-Building

Build log for relion (3.1.3-3) on armhf
