relion →
3.1.3-2 →
armhf → 2022-10-04 11:14:19
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| relion 3.1.3-2 (armhf) Tue, 04 Oct 2022 09:18:21 +0000 |
+==============================================================================+
Package: relion
Version: 3.1.3-2
Source Version: 3.1.3-2
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-7702c454-d183-4695-bf88-544fa98ea5c9' 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 [13.3 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.2 MB]
Fetched 27.5 MB in 29s (955 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 2359 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main relion 3.1.3-2 (dsc) [2136 B]
Get:2 http://172.17.4.1/private bookworm-staging/main relion 3.1.3-2 (tar) [2345 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main relion 3.1.3-2 (diff) [11.1 kB]
Fetched 2359 kB in 0s (8008 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/relion-apzZh9/relion-3.1.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/relion-apzZh9' 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-1TQ11d/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-1TQ11d/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-1TQ11d/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-1TQ11d/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2630 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 libpam-cap netbase 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 6 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12808 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-1TQ11d/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-1TQ11d/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ Sources [525 B]
Get:5 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ Packages [603 B]
Fetched 2461 B in 1s (2916 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 libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common 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
libcurl3-gnutls 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 libicu71 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 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 ucf x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
cmake-format dh-make 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 openmpi-doc pciutils lm-sensors
gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less www-browser opencl-icd
gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass
libmail-box-perl
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 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-elpa-helper dh-strip-nondeterminism dwz
emacsen-common 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
libcurl3-gnutls 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 libicu71 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 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
0 upgraded, 170 newly installed, 0 to remove and 6 not upgraded.
Need to get 89.0 MB of archives.
After this operation, 358 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-1TQ11d/apt_archive ./ sbuild-build-depends-relion-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1 [137 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-3 [1364 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-7 [60.7 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-7 [475 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.6-1 [109 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libcbor0.8 armhf 0.8.0-2 [22.8 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libfido2-1 armhf 1.11.0-1+b1 [66.7 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf openssh-client armhf 1:9.0p1-1+b2 [890 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.6.0-1 [306 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.85.0-1 [325 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.9-1 [83.3 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-4 [66.7 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.44.2-1+rpi1 [125 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.11 [11.4 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.24.2-1 [2019 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.24.2-1 [3661 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.9.1 [196 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.9.1 [1071 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.38-2 [273 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libxfixes3 armhf 1:6.0.0-1 [21.0 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libxcursor1 armhf 1:1.2.1-1 [38.0 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libxft2 armhf 2.3.4-1 [50.2 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libxinerama1 armhf 2:1.1.4-3 [17.4 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libfltk1.3 armhf 1.3.8-5 [501 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libfltk-forms1.3 armhf 1.3.8-5 [52.1 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libfltk-images1.3 armhf 1.3.8-5 [63.5 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf fluid armhf 1.3.8-5 [210 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-3+rpi1 [238 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-12-dev armhf 12.2.0-3+rpi1 [285 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf gfortran-12 armhf 12.2.0-3+rpi1 [7509 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.7.0-0.2 [55.0 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.2 [152 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libibverbs1 armhf 42.0-1 [53.7 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf ibverbs-providers armhf 42.0-1 [28.8 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-6 [496 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.85.0-1 [320 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.12-1 [60.5 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.12-1 [51.8 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libdrm-common all 2.4.113-2+rpi1 [15.8 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libdrm2 armhf 2.4.113-2+rpi1 [41.6 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libdrm-amdgpu1 armhf 2.4.113-2+rpi1 [28.4 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libdrm-nouveau2 armhf 2.4.113-2+rpi1 [26.0 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libdrm-radeon1 armhf 2.4.113-2+rpi1 [29.7 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-5+b1 [166 kB]
Ign:96 http://172.17.4.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-5+b1
Get:97 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:98 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:99 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:100 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:101 http://172.17.4.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-5+b1 [280 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf librdmacm1 armhf 42.0-1 [60.3 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-3 [310 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libfltk-cairo1.3 armhf 1.3.8-5 [46.6 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libglvnd0 armhf 1.5.0-1 [51.5 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libglapi-mesa armhf 22.2.0-1+rpi1 [84.6 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libx11-xcb1 armhf 2:1.8.1-2 [203 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf libxcb-glx0 armhf 1.15-1 [121 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libxcb-present0 armhf 1.15-1 [105 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libxcb-sync1 armhf 1.15-1 [108 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libxcb-xfixes0 armhf 1.15-1 [109 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libxshmfence1 armhf 1.3-1 [8636 B]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.1 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf libz3-4 armhf 4.8.12-1 [5758 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libllvm14 armhf 1:14.0.6-2+rpi1 [19.5 MB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libsensors-config all 1:3.6.0-7 [32.3 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libsensors5 armhf 1:3.6.0-7 [49.6 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libgl1-mesa-dri armhf 22.2.0-1+rpi1 [5593 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf libglx-mesa0 armhf 22.2.0-1+rpi1 [171 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf libglx0 armhf 1.5.0-1 [32.4 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf libgl1 armhf 1.5.0-1 [91.8 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf libfltk-gl1.3 armhf 1.3.8-5 [72.9 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf x11proto-dev all 2022.1-1 [599 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf libxcb1-dev armhf 1.15-1 [175 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf libx11-dev armhf 2:1.8.1-2 [780 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libfltk1.3-dev armhf 1.3.8-5 [807 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf libhwloc15 armhf 2.8.0-1 [130 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.15-1 [22.3 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.15-1 [35.5 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.7-4 [399 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.7-4 [161 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.8.0-1 [202 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.16-3 [51.2 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf libxnvctrl0 armhf 470.141.03-1 [26.3 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-3 [39.9 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.8.0-1 [20.4 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.7.0-0.2 [93.4 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.7.0-0.2 [163 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf libibverbs-dev armhf 42.0-1 [188 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf libjbig-dev armhf 2.1-3.1+b2 [27.7 kB]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf liblerc4 armhf 4.0.0+ds-1 [121 kB]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf liblerc-dev armhf 4.0.0+ds-1 [136 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2.1 [218 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf libpmix2 armhf 4.2.0+really.4.1.2-3 [487 kB]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.4-1+rpi1 [1794 kB]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf openmpi-common all 4.1.4-1+rpi1 [183 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf libpmix-dev armhf 4.2.0+really.4.1.2-3 [654 kB]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.4-1+rpi1 [211 kB]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.4-1+rpi1 [940 kB]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2 [237 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.4.0-4 [290 kB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf libtiffxx5 armhf 4.4.0-4 [145 kB]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf libtiff-dev armhf 4.4.0-4 [401 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-5+b1 [166 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libuchardet0:armhf.
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Preparing to unpack .../000-libuchardet0_0.0.7-1_armhf.deb ...
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Unpacking man-db (2.10.2-3) ...
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Selecting previously unselected package libprocps8:armhf.
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Unpacking libprocps8:armhf (2:3.3.17-7) ...
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Unpacking procps (2:3.3.17-7) ...
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Unpacking libmagic-mgc (1:5.41-4) ...
Selecting previously unselected package libmagic1:armhf.
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Unpacking libmagic1:armhf (1:5.41-4) ...
Selecting previously unselected package file.
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Unpacking file (1:5.41-4) ...
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Preparing to unpack .../011-gettext-base_0.21-9_armhf.deb ...
Unpacking gettext-base (0.21-9) ...
Selecting previously unselected package libmd0:armhf.
Preparing to unpack .../012-libmd0_1.0.4-2_armhf.deb ...
Unpacking libmd0:armhf (1.0.4-2) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../013-libbsd0_0.11.6-1_armhf.deb ...
Unpacking libbsd0:armhf (0.11.6-1) ...
Selecting previously unselected package libedit2:armhf.
Preparing to unpack .../014-libedit2_3.1-20210910-1_armhf.deb ...
Unpacking libedit2:armhf (3.1-20210910-1) ...
Selecting previously unselected package libcbor0.8:armhf.
Preparing to unpack .../015-libcbor0.8_0.8.0-2_armhf.deb ...
Unpacking libcbor0.8:armhf (0.8.0-2) ...
Selecting previously unselected package libfido2-1:armhf.
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Unpacking libfido2-1:armhf (1.11.0-1+b1) ...
Selecting previously unselected package openssh-client.
Preparing to unpack .../017-openssh-client_1%3a9.0p1-1+b2_armhf.deb ...
Unpacking openssh-client (1:9.0p1-1+b2) ...
Selecting previously unselected package ucf.
Preparing to unpack .../018-ucf_3.0043_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0043) ...
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Unpacking m4 (1.4.19-1) ...
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Unpacking autoconf (2.71-2) ...
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Unpacking autotools-dev (20220109.1) ...
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Unpacking autopoint (0.21-9) ...
Selecting previously unselected package libicu71:armhf.
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Unpacking libicu71:armhf (71.1-3) ...
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Unpacking libxml2:armhf (2.9.14+dfsg-1) ...
Selecting previously unselected package libarchive13:armhf.
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Unpacking libarchive13:armhf (3.6.0-1) ...
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Unpacking libpsl5:armhf (0.21.0-1.2) ...
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
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Unpacking libcurl4:armhf (7.85.0-1) ...
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Selecting previously unselected package libjsoncpp25:armhf.
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Unpacking libjsoncpp25:armhf (1.9.5-4) ...
Selecting previously unselected package librhash0:armhf.
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Unpacking librhash0:armhf (1.4.3-3) ...
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Unpacking libuv1:armhf (1.44.2-1+rpi1) ...
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Unpacking dh-elpa-helper (2.0.11) ...
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Unpacking emacsen-common (3.0.4) ...
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Unpacking cmake-data (3.24.2-1) ...
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Unpacking cmake (3.24.2-1) ...
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Unpacking libdebhelper-perl (13.9.1) ...
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Unpacking libelf1:armhf (0.187-2+rpi2) ...
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Unpacking dwz (0.14-1) ...
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Unpacking gettext (0.21-9) ...
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Unpacking po-debconf (1.0.21+nmu1) ...
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Unpacking debhelper (13.9.1) ...
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Unpacking libpng16-16:armhf (1.6.38-2) ...
Selecting previously unselected package libfreetype6:armhf.
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Unpacking libtiff5:armhf (4.4.0-4) ...
Selecting previously unselected package libtiffxx5:armhf.
Preparing to unpack .../167-libtiffxx5_4.4.0-4_armhf.deb ...
Unpacking libtiffxx5:armhf (4.4.0-4) ...
Selecting previously unselected package libtiff-dev:armhf.
Preparing to unpack .../168-libtiff-dev_4.4.0-4_armhf.deb ...
Unpacking libtiff-dev:armhf (4.4.0-4) ...
Selecting previously unselected package sbuild-build-depends-relion-dummy.
Preparing to unpack .../169-sbuild-build-depends-relion-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-relion-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.4.9-1) ...
Setting up libpipeline1:armhf (1.5.6-3) ...
Setting up libpixman-1-0:armhf (0.40.0-1) ...
Setting up libicu71:armhf (71.1-3) ...
Setting up libpciaccess0:armhf (0.16-3) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up libfftw3-single3:armhf (3.3.8-2) ...
Setting up liblerc4:armhf (4.0.0+ds-1) ...
Setting up bsdextrautils (2.38.1-1) ...
Setting up libmagic-mgc (1:5.41-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglvnd0:armhf (1.5.0-1) ...
Setting up libcbor0.8:armhf (0.8.0-2) ...
Setting up libdebhelper-perl (13.9.1) ...
Setting up libbrotli1:armhf (1.0.9-2+b2) ...
Setting up libsensors-config (1:3.6.0-7) ...
Setting up libnghttp2-14:armhf (1.50.0-1) ...
Setting up libmagic1:armhf (1:5.41-4) ...
Setting up libdeflate0:armhf (1.12-1) ...
Setting up gettext-base (0.21-9) ...
Setting up m4 (1.4.19-1) ...
Setting up file (1:5.41-4) ...
Setting up libpthread-stubs0-dev:armhf (0.4-1) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up xtrans-dev (1.4.0-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libz3-4:armhf (4.8.12-1) ...
Setting up libuv1:armhf (1.44.2-1+rpi1) ...
Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
Setting up emacsen-common (3.0.4) ...
Setting up libx11-data (2:1.8.1-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:2.1.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up dh-elpa-helper (2.0.11) ...
Setting up libncurses6:armhf (6.3+20220423-2) ...
Setting up libpng16-16:armhf (1.6.38-2) ...
Setting up libhwloc15:armhf (2.8.0-1) ...
Setting up libevent-core-2.1-7:armhf (2.1.12-stable-5+b1) ...
Setting up libevent-2.1-7:armhf (2.1.12-stable-5+b1) ...
Setting up autopoint (0.21-9) ...
Setting up libjsoncpp25:armhf (1.9.5-4) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up ucf (3.0043) ...
Setting up libsensors5:armhf (1:3.6.0-7) ...
Setting up liblerc-dev:armhf (4.0.0+ds-1) ...
Setting up libltdl7:armhf (2.4.7-4) ...
Setting up libfftw3-double3:armhf (3.3.8-2) ...
Setting up libglapi-mesa:armhf (22.2.0-1+rpi1) ...
Setting up libgfortran5:armhf (12.2.0-3+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up libwebp7:armhf (1.2.2-2) ...
Setting up liblzma-dev:armhf (5.2.5-2.1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-4.1) ...
Setting up libnuma1:armhf (2.0.15-1) ...
Setting up libmd0:armhf (1.0.4-2) ...
Setting up ocl-icd-libopencl1:armhf (2.2.14-3) ...
Setting up libxshmfence1:armhf (1.3-1) ...
Setting up librhash0:armhf (1.4.3-3) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libnl-3-200:armhf (3.7.0-0.2) ...
Setting up openmpi-common (4.1.4-1+rpi1) ...
Setting up libsub-override-perl (0.09-3) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up xorg-sgml-doctools (1:1.11-1.1) ...
Setting up cmake-data (3.24.2-1) ...
Setting up libtiff5:armhf (4.4.0-4) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libfido2-1:armhf (1.11.0-1+b1) ...
Setting up libbsd0:armhf (0.11.6-1) ...
Setting up libdeflate-dev:armhf (1.12-1) ...
Setting up libdrm-common (2.4.113-2+rpi1) ...
Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up libprocps8:armhf (2:3.3.17-7) ...
Setting up libtiffxx5:armhf (4.4.0-4) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-5+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-5+b1) ...
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-9) ...
Setting up libxcb-xfixes0:armhf (1.15-1) ...
Setting up libtool (2.4.7-4) ...
Setting up libarchive13:armhf (3.6.0-1) ...
Setting up libxcb-render0:armhf (1.15-1) ...
Setting up libfftw3-bin (3.3.8-2) ...
Setting up fontconfig-config (2.13.1-4.5) ...
Setting up libxcb-glx0:armhf (1.15-1) ...
Setting up libedit2:armhf (3.1-20210910-1) ...
Setting up libjpeg-dev:armhf (1:2.1.2-1) ...
Setting up libjbig-dev:armhf (2.1-3.1+b2) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-5+b1) ...
Setting up libcurl3-gnutls:armhf (7.85.0-1) ...
Setting up libgfortran-12-dev:armhf (12.2.0-3+rpi1) ...
Setting up libxcb-shm0:armhf (1.15-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnuma-dev:armhf (2.0.15-1) ...
Setting up libnl-route-3-200:armhf (3.7.0-0.2) ...
Setting up libxcb-present0:armhf (1.15-1) ...
Setting up dh-autoreconf (20) ...
Setting up libltdl-dev:armhf (2.4.7-4) ...
Setting up gfortran-12 (12.2.0-3+rpi1) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libfreetype6:armhf (2.12.1+dfsg-3) ...
Setting up libtiff-dev:armhf (4.4.0-4) ...
Setting up libxcb-sync1:armhf (1.15-1) ...
Setting up libevent-dev (2.1.12-stable-5+b1) ...
Setting up libxcb-dri2-0:armhf (1.15-1) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up libllvm14:armhf (1:14.0.6-2+rpi1) ...
Setting up libdrm2:armhf (2.4.113-2+rpi1) ...
Setting up dwz (0.14-1) ...
Setting up libnl-3-dev:armhf (3.7.0-0.2) ...
Setting up groff-base (1.22.4-8) ...
Setting up procps (2:3.3.17-7) ...
Setting up libcurl4:armhf (7.85.0-1) ...
Setting up libx11-6:armhf (2:1.8.1-2) ...
Setting up libhwloc-dev:armhf (2.8.0-1) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up libdrm-amdgpu1:armhf (2.4.113-2+rpi1) ...
Setting up libxcb-dri3-0:armhf (1.15-1) ...
Setting up libx11-xcb1:armhf (2:1.8.1-2) ...
Setting up libibverbs1:armhf (42.0-1) ...
Setting up libdrm-nouveau2:armhf (2.4.113-2+rpi1) ...
Setting up libxrender1:armhf (1:0.9.10-1.1) ...
Setting up ibverbs-providers:armhf (42.0-1) ...
Setting up libdrm-radeon1:armhf (2.4.113-2+rpi1) ...
Setting up openssh-client (1:9.0p1-1+b2) ...
update-alternatives: using /usr/bin/ssh to provide /usr/bin/rsh (rsh) in auto mode
update-alternatives: using /usr/bin/slogin to provide /usr/bin/rlogin (rlogin) in auto mode
update-alternatives: using /usr/bin/scp to provide /usr/bin/rcp (rcp) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libgl1-mesa-dri:armhf (22.2.0-1+rpi1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up man-db (2.10.2-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ...
Setting up libxnvctrl0:armhf (470.141.03-1) ...
Setting up libnl-route-3-dev:armhf (3.7.0-0.2) ...
Setting up libxfixes3:armhf (1:6.0.0-1) ...
Setting up libxinerama1:armhf (2:1.1.4-3) ...
Setting up cmake (3.24.2-1) ...
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 (13.9.1) ...
Setting up libibverbs-dev:armhf (42.0-1) ...
Setting up libhwloc-plugins:armhf (2.8.0-1) ...
Setting up libgl1:armhf (1.5.0-1) ...
Setting up libfabric1:armhf (1.11.0-3) ...
Setting up libpmix2:armhf (4.2.0+really.4.1.2-3) ...
Setting up libopenmpi3:armhf (4.1.4-1+rpi1) ...
Setting up libpmix-dev:armhf (4.2.0+really.4.1.2-3) ...
Setting up openmpi-bin (4.1.4-1+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 (4.1.4-1+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 (2.35-1+rpi1) ...
Processing triggers for sgml-base (1.30) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Setting up x11proto-dev (2022.1-1) ...
Setting up libxft2:armhf (2.3.4-1) ...
Setting up libxau-dev:armhf (1:1.0.9-1) ...
Setting up libfltk1.3:armhf (1.3.8-5) ...
Setting up libfltk-gl1.3:armhf (1.3.8-5) ...
Setting up libfltk-images1.3:armhf (1.3.8-5) ...
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) ...
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) ...
Setting up fluid (1.3.8-5) ...
Setting up libfltk1.3-dev:armhf (1.3.8-5) ...
Setting up sbuild-build-depends-relion-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.35-1+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.39-3+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-1+rpi1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-3+rpi1 binutils-arm-linux-gnueabihf_2.39-3+rpi1 binutils-common_2.39-3+rpi1 bsdextrautils_2.38.1-1 bsdutils_1:2.38.1-1 build-essential_12.9 bzip2_1.0.8-5+b2 cmake_3.24.2-1 cmake-data_3.24.2-1 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.9.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-elpa-helper_2.0.11 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.6~rc1-1 emacsen-common_3.0.4 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 fluid_1.3.8-5 fontconfig-config_2.13.1-4.5 fonts-dejavu-core_2.37-2 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+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_0.21-9 gettext-base_0.21-9 gfortran-12_12.2.0-3+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_1.22.4-8 gzip_1.12-1 hostname_3.23 ibverbs-providers_42.0-1 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.2 libarchive-zip-perl_1.68-1 libarchive13_3.6.0-1 libasan8_12.2.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-3+rpi1 libblkid1_2.38.1-1 libbrotli1_1.0.9-2+b2 libbsd0_0.11.6-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-1+rpi1 libc-dev-bin_2.35-1+rpi1 libc6_2.35-1+rpi1 libc6-dev_2.35-1+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_12.2.0-3+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-3+rpi1 libctf0_2.39-3+rpi1 libcurl3-gnutls_7.85.0-1 libcurl4_7.85.0-1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.9.1 libdeflate-dev_1.12-1 libdeflate0_1.12-1 libdpkg-perl_1.21.9+rpi1 libdrm-amdgpu1_2.4.113-2+rpi1 libdrm-common_2.4.113-2+rpi1 libdrm-nouveau2_2.4.113-2+rpi1 libdrm-radeon1_2.4.113-2+rpi1 libdrm2_2.4.113-2+rpi1 libedit2_3.1-20210910-1 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_2.4.9-1 libext2fs2_1.46.6~rc1-1 libfabric1_1.11.0-3 libfakeroot_1.29-1 libffi8_3.4.2-4 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfido2-1_1.11.0-1+b1 libfile-stripnondeterminism-perl_1.13.0-1 libfltk-cairo1.3_1.3.8-5 libfltk-forms1.3_1.3.8-5 libfltk-gl1.3_1.3.8-5 libfltk-images1.3_1.3.8-5 libfltk1.3_1.3.8-5 libfltk1.3-dev_1.3.8-5 libfontconfig1_2.13.1-4.5 libfreetype6_2.12.1+dfsg-3 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-2 libgdbm6_1.23-2 libgfortran-12-dev_12.2.0-3+rpi1 libgfortran5_12.2.0-3+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 libgnutls30_3.7.7-2 libgomp1_12.2.0-3+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 libicu71_71.1-3 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-2.5-0_2.5.13+dfsg-1 liblerc-dev_4.0.0+ds-1 liblerc4_4.0.0+ds-1 libllvm14_1:14.0.6-2+rpi1 libltdl-dev_2.4.7-4 libltdl7_2.4.7-4 liblz4-1_1.9.4-1+rpi1 liblzma-dev_5.2.5-2.1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 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_4.1.4-1+rpi1 libopenmpi3_4.1.4-1+rpi1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-2 libpam-modules-bin_1.5.2-2 libpam-runtime_1.5.2-2 libpam0g_1.5.2-2 libpciaccess0_0.16-3 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libpipeline1_1.5.6-3 libpixman-1-0_0.40.0-1 libpmix-dev_4.2.0+really.4.1.2-3 libpmix2_4.2.0+really.4.1.2-3 libpng16-16_1.6.38-2 libprocps8_2:3.3.17-7 libpsl5_0.21.0-1.2 libpthread-stubs0-dev_0.4-1 librdmacm1_42.0-1 libreadline8_8.2~rc2-2 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 libsensors5_1:3.6.0-7 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1 libsqlite3-0_3.39.3-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.5-2 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-3 libsystemd0_251.4-3+rpi1 libtasn1-6_4.19.0-2 libtiff-dev_4.4.0-4 libtiff5_4.4.0-4 libtiffxx5_4.4.0-4 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_2.4.7-4 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.4-3+rpi1 libunistring2_1.0-1 libuuid1_2.38.1-1 libuv1_1.44.2-1+rpi1 libwebp7_1.2.2-2 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 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_1:6.0.0-1 libxft2_2.3.4-1 libxinerama1_2:1.1.4-3 libxml2_2.9.14+dfsg-1 libxnvctrl0_470.141.03-1 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_4.8.12-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.10.2-3 mawk_1.3.4.20200120-3.1 mount_2.38.1-1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 ocl-icd-libopencl1_2.2.14-3 openmpi-bin_4.1.4-1+rpi1 openmpi-common_4.1.4-1+rpi1 openssh-client_1:9.0p1-1+b2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 procps_2:3.3.17-7 raspbian-archive-keyring_20120528.2 readline-common_8.2~rc2-2 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_1.30 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 ucf_3.0043 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 x11proto-dev_2022.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-2.1 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.bHTatxTi/trustedkeys.kbx': General error
gpgv: Signature made Thu Sep 29 11:29:15 2022 UTC
gpgv: using RSA key EBF30A30A8D9C63BDA44C6945FB33F9359E9ED08
gpgv: issuer "anbe@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./relion_3.1.3-2.dsc
dpkg-source: info: extracting relion in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking relion_3.1.3.orig.tar.gz
dpkg-source: info: unpacking relion_3.1.3-2.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-7702c454-d183-4695-bf88-544fa98ea5c9
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package relion
dpkg-buildpackage: info: source version 3.1.3-2
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-3.24/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-3.24/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-3.24/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-3.24/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
/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>> /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color=
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 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
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'
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_plottable /<<PKGBUILDDIR>>/build/bin/relion_star_plottable
[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o
[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o
[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_loopheader /<<PKGBUILDDIR>>/build/bin/relion_star_loopheader
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
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
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
/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 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,
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 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>::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); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/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::__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 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 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 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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::_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); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<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::__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); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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 '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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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>::
| ^~~~~~~~~~~~~~~~~~~
[ 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
/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
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
[ 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>::
| ^~~~~~~~~~~~~~~~~~~
/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 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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;
| ^~~~~~
/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);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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 = {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 /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 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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
[ 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/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
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;
| ^~~~~~
/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
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 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 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/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
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/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 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 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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
[ 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
/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>::
| ^~~~~~~~~~~~~~~~~~~
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;
| ^~~~~~
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;
| ^~~~~~
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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 /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 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 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>::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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/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>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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
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
[ 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
[ 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
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/__/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
[ 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/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);
| ~~~~~~~
/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/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
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/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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
/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 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 /<<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 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: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 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);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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
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_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 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>::
| ^~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/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>::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 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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
[ 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.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/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
[ 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 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;
| ^~
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
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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>::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);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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 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;
| ^~~~~~
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 /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>::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);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::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/__/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
[ 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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
/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 /<<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
[ 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 /<<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);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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;
| ^~~~~~
/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 /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
[ 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
[ 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 /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 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 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 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 '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<>());
| ~~~~~~~~~~~~~~~
/<<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/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
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/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
[ 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
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;
| ^~~~~~
[ 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
[ 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/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;
| ^~~~~~
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;
| ^~~~~~
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
[ 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;
| ^~~~~~
[ 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
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/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
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;
| ^~~~~~
[ 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/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;
| ^~~~~~
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/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
[ 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
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/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
[ 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/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;
| ^~~~~~
[ 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/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;
| ^~~~~~
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
[ 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
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/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
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;
| ^~~~~~
[ 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
/<<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
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;
| ^~~~~~
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;
| ^~~~~~
[ 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
[ 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 /<<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;
| ^~~~~~
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 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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 /<<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
[ 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/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;
| ^~~~~~
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/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 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;
| ^~~~~~
[ 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
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/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
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;
| ^~~~~~
[ 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/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;
| ^~~~~~
[ 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/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;
| ^~~~~~
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;
| ^~~~~~
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>::
| ^~~~~~~~~~~~~~~~~~~
[ 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 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 /<<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 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 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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
[ 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/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;
| ^~~~~~
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
[ 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 /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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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;
| ^~~~~~
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/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
[ 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
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;
| ^~~~~~
[ 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
[ 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/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;
| ^~~~~~
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
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;
| ^~~~~~
[ 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 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 /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::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 /<<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
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/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsyevq3.c
[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.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/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsyevv3.c
[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.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/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsytrd3.c
[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.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/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
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_lib.dir/link.txt --verbose=1
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CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o
/usr/bin/ranlib ../../lib/librelion_lib.a
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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_gui_lib.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/align_symmetry.dir/DependInfo.cmake --color=
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=
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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/autopick.dir/DependInfo.cmake --color=
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[ 53%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o
[ 54%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o
[ 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/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
[ 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/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
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
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
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/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/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;
| ^~~~~~
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;
| ^~~~~~
/<<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
[ 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 56%] Built target autopick_mpi
[ 56%] 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_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'
[ 56%] 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
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_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
[ 57%] 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'
[ 57%] Built target align_symmetry
[ 58%] 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;
| ^~~~~~
/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'
[ 58%] 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;
| ^~~~~~
[ 58%] 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'
[ 58%] Built target convert_to_tiff
[ 58%] 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/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'
[ 59%] 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;
| ^~~~~~
[ 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
[ 60%] 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
/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'
[ 60%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 60%] Built target convert_to_tiff_mpi
/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'
[ 60%] 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
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;
| ^~~~~~
/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
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;
| ^~~~~~
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;
| ^~~~~~
[ 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
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
[ 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
[ 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
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;
| ^~~~~~
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
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;
| ^~~~~~
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;
| ^~~~~~
[ 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
[ 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 64%] 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'
[ 64%] 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
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/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;
| ^~~~~~
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
[ 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] 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=
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'
[ 66%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target demodulate
/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'
[ 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
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_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
[ 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 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
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_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
[ 68%] 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'
[ 68%] Built target flex_analyse
/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_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'
[ 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 find_tiltpairs
/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;
| ^~~~~~
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;
| ^~~~~~
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;
| ^~~~~~
[ 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
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/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
[ 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
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
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_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 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/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;
| ^~~~~~
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;
| ^~~~~~
[ 73%] Linking CXX executable ../../bin/relion
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion.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/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 74%] Built target relion
[ 74%] 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/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=
/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
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'
[ 74%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_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/mask_create.dir/mask_create.cpp.o -MF CMakeFiles/mask_create.dir/mask_create.cpp.o.d -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /<<PKGBUILDDIR>>/src/apps/mask_create.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 74%] Built target manualpick
/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'
[ 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
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;
| ^~~~~~
[ 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
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
[ 76%] 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
[ 76%] 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'
[ 76%] Built target motion_refine
/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'
[ 76%] 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_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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
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;
| ^~~~~~
[ 77%] Built target mask_create
/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend
/<<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]: 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 image_handler
/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
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;
| ^~~~~~
[ 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
[ 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 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
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
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;
| ^~~~~~
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;
| ^~~~~~
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;
| ^~~~~~
[ 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
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/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;
| ^~~~~~
[ 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
[ 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target particle_subtract
/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'
[ 83%] 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_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'
[ 83%] Built target particle_subtract_mpi
/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target particle_symmetry_expand
/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
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;
| ^~~~~~
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 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
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 83%] 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
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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
[ 84%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/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
[ 84%] 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'
[ 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target pipeliner
/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target particle_reposition
/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'
[ 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
[ 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
/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
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]: 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'
[ 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/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;
| ^~~~~~
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;
| ^~~~~~
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;
| ^~~~~~
/<<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/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;
| ^~~~~~
[ 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 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
[ 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
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=
/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
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
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_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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 89%] 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'
[ 89%] 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
[ 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_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 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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;
| ^~~~~~
[ 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
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=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 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
[ 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
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;
| ^~~~~~
[ 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
/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]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target project
/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=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
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%] Built target refine_mpi
/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend
[ 91%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o
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=
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'
/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'
[ 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=
[ 92%] 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
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'
/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
[ 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
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;
| ^~~~~~
[ 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 94%] 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'
[ 94%] 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
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;
| ^~~~~~
[ 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 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 96%] 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'
[ 97%] 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
[ 98%] 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
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;
| ^~~~~~
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/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
[ 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 /<<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;
| ^~~~~~
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 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>::
| ^~~~~~~~~~~~~~~~~~~
[ 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[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
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
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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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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
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/usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend
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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=
Consolidate compiler generated dependencies of target relion_lib
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/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=
Consolidate compiler generated dependencies of target relion_gui_lib
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=
Consolidate compiler generated dependencies of target align_symmetry
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=
Consolidate compiler generated dependencies of target autopick
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=
Consolidate compiler generated dependencies of target autopick_mpi
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=
Consolidate compiler generated dependencies of target convert_star
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=
Consolidate compiler generated dependencies of target convert_to_tiff
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=
Consolidate compiler generated dependencies of target convert_to_tiff_mpi
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=
Consolidate compiler generated dependencies of target ctf_mask_test
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=
Consolidate compiler generated dependencies of target ctf_refine
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=
Consolidate compiler generated dependencies of target ctf_refine_mpi
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=
Consolidate compiler generated dependencies of target ctf_toolbox
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=
Consolidate compiler generated dependencies of target demodulate
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=
Consolidate compiler generated dependencies of target display
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=
Consolidate compiler generated dependencies of target estimate_gain
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=
Consolidate compiler generated dependencies of target external_reconstruct
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=
Consolidate compiler generated dependencies of target find_tiltpairs
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=
Consolidate compiler generated dependencies of target flex_analyse
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=
Consolidate compiler generated dependencies of target flex_analyse_mpi
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=
Consolidate compiler generated dependencies of target helix_inimodel2d
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=
Consolidate compiler generated dependencies of target helix_toolbox
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=
Consolidate compiler generated dependencies of target image_handler
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=
Consolidate compiler generated dependencies of target import
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=
Consolidate compiler generated dependencies of target localsym
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=
Consolidate compiler generated dependencies of target localsym_mpi
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=
Consolidate compiler generated dependencies of target relion
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=
Consolidate compiler generated dependencies of target manualpick
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=
Consolidate compiler generated dependencies of target mask_create
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=
Consolidate compiler generated dependencies of target merge_particles
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=
Consolidate compiler generated dependencies of target motion_refine
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=
Consolidate compiler generated dependencies of target motion_refine_mpi
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=
Consolidate compiler generated dependencies of target mrc2vtk
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=
Consolidate compiler generated dependencies of target particle_FCC
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=
Consolidate compiler generated dependencies of target particle_reposition
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=
Consolidate compiler generated dependencies of target particle_select
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=
Consolidate compiler generated dependencies of target particle_subtract
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=
Consolidate compiler generated dependencies of target particle_subtract_mpi
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=
Consolidate compiler generated dependencies of target particle_symmetry_expand
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=
Consolidate compiler generated dependencies of target pipeliner
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=
Consolidate compiler generated dependencies of target plot_delocalisation
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=
Consolidate compiler generated dependencies of target postprocess
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=
Consolidate compiler generated dependencies of target postprocess_mpi
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=
Consolidate compiler generated dependencies of target prepare_subtomo
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=
Consolidate compiler generated dependencies of target preprocess
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=
Consolidate compiler generated dependencies of target preprocess_mpi
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=
Consolidate compiler generated dependencies of target project
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=
Consolidate compiler generated dependencies of target reconstruct
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=
Consolidate compiler generated dependencies of target reconstruct_mpi
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'
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[ 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=
Consolidate compiler generated dependencies of target refine
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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=
Consolidate compiler generated dependencies of target refine_mpi
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make[4]: Entering directory '/<<PKGBUILDDIR>>/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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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'
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=
Consolidate compiler generated dependencies of target run_ctffind_mpi
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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/run_motioncorr.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/run_motioncorr_mpi.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target run_motioncorr_mpi
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make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr_mpi.dir/build'.
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[ 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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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=
Consolidate compiler generated dependencies of target stack_create
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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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[ 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=
Consolidate compiler generated dependencies of target tiltpair_plot
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/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make 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=
Consolidate compiler generated dependencies of target tomo_test
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/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'.
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[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'.
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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_align_symmetry
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff
-- 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_flex_analyse
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_find_tiltpairs
-- 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
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_manualpick
-- 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_motion_refine
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mask_create
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_image_handler
-- 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_subtract
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess
-- 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_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_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/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-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-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_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_reconstruct 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_manualpick debian/relion-gui/usr/bin/relion_display 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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_ctf_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_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/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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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/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_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_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_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_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_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_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_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_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_pipeliner 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_preprocess_mpi debian/relion/usr/bin/relion_ctf_refine debian/relion/usr/bin/relion_run_ctffind_mpi debian/relion/usr/bin/relion_reconstruct debian/relion/usr/bin/relion_prepare_subtomo debian/relion/usr/bin/relion_plot_delocalisation debian/relion/usr/bin/relion_motion_refine_mpi debian/relion/usr/bin/relion_flex_analyse debian/relion/usr/bin/relion_align_symmetry debian/relion/usr/bin/relion_external_reconstruct debian/relion/usr/bin/relion_merge_particles debian/relion/usr/bin/relion_flex_analyse_mpi debian/relion/usr/bin/relion_motion_refine debian/relion/usr/bin/relion_particle_symmetry_expand debian/relion/usr/bin/relion_autopick debian/relion/usr/bin/relion_particle_reposition debian/relion/usr/bin/relion_convert_to_tiff debian/relion/usr/bin/relion_import debian/relion/usr/bin/relion_demodulate debian/relion/usr/bin/relion_convert_star debian/relion/usr/bin/relion_localsym debian/relion/usr/bin/relion_particle_select debian/relion/usr/bin/relion_ctf_refine_mpi debian/relion/usr/bin/relion_autopick_mpi debian/relion/usr/bin/relion_postprocess debian/relion/usr/bin/relion_preprocess debian/relion/usr/bin/relion_star_handler debian/relion/usr/bin/relion_find_tiltpairs debian/relion/usr/bin/relion_particle_FCC debian/relion/usr/bin/relion_run_ctffind debian/relion/usr/bin/relion_particle_subtract_mpi debian/relion/usr/bin/relion_ctf_toolbox debian/relion/usr/bin/relion_helix_toolbox debian/relion/usr/bin/relion_postprocess_mpi debian/relion/usr/bin/relion_refine_mpi debian/relion/usr/bin/relion_run_motioncorr_mpi debian/relion/usr/bin/relion_mrc2vtk debian/relion/usr/bin/relion_helix_inimodel2d debian/relion/usr/bin/relion_convert_to_tiff_mpi debian/relion/usr/bin/relion_stack_create debian/relion/usr/bin/relion_particle_subtract debian/relion/usr/bin/relion_estimate_gain debian/relion/usr/bin/relion_image_handler debian/relion/usr/bin/relion_tomo_test debian/relion/usr/bin/relion_run_motioncorr debian/relion/usr/bin/relion_localsym_mpi debian/relion/usr/bin/relion_ctf_mask_test debian/relion/usr/bin/relion_refine debian/relion/usr/bin/relion_tiltpair_plot debian/relion/usr/bin/relion_reposition debian/relion/usr/bin/relion_reconstruct_mpi debian/relion/usr/bin/relion_mask_create debian/relion/usr/bin/relion_project debian/relion/usr/bin/relion_scheduler debian/relion/usr/bin/relion_pipeliner 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-dbgsym' in '../relion-dbgsym_3.1.3-2_armhf.deb'.
dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-2_armhf.deb'.
dpkg-deb: building package 'relion' in '../relion_3.1.3-2_armhf.deb'.
dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.3-2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../relion_3.1.3-2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../relion_3.1.3-2_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 2022-10-04T11:12:03Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
relion_3.1.3-2_armhf.changes:
-----------------------------
Format: 1.8
Date: Thu, 29 Sep 2022 13:27:08 +0200
Source: relion
Binary: relion relion-dbgsym relion-gui relion-gui-dbgsym
Architecture: armhf
Version: 3.1.3-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Beckmann <anbe@debian.org>
Description:
relion - toolkit for 3D reconstructions in cryo-electron microscopy
relion-gui - toolkit for 3D reconstructions in cryo-electron microscopy (gui a
Closes: 995224
Changes:
relion (3.1.3-2) unstable; urgency=medium
.
[ Andreas Beckmann ]
* Team upload.
* Cherry-pick upstream fixes related to cub. (Closes: #995224)
* Simplify debian/rules.
* Fix missing hardening flags.
* Build for Architecture: any.
* Standards-Version: 4.6.1.
* Fix some typos found by Lintian.
.
[ Andreas Tille ]
* Enable uscan to create a sensible download name
Checksums-Sha1:
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10bb519e186991099d549352a4ea1586aa931488 19908572 relion-gui-dbgsym_3.1.3-2_armhf.deb
5c6d0021316d723702bf8bf1dfa31244369b1581 853076 relion-gui_3.1.3-2_armhf.deb
83582cf4c1ec5b86d8ac71d1f770446d88e19050 10005 relion_3.1.3-2_armhf.buildinfo
da67ecb37b68348856b535c1fd7ed870d3e4b663 9356604 relion_3.1.3-2_armhf.deb
Checksums-Sha256:
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7803417b780d2496a83f687eec2af726cfb8cf29dc2c56e11bb8adf5463eb679 853076 relion-gui_3.1.3-2_armhf.deb
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Files:
6e7b294e5ca3085eb8e0cf4f264d492d 329862800 debug optional relion-dbgsym_3.1.3-2_armhf.deb
7ce88a3ac026d8afbe23c3a0b8da1837 19908572 debug optional relion-gui-dbgsym_3.1.3-2_armhf.deb
77596638c50643d6eaeaeaf9f002717a 853076 science optional relion-gui_3.1.3-2_armhf.deb
74afd86d817a4eb14a1a1741fed406b9 10005 science optional relion_3.1.3-2_armhf.buildinfo
3864e251bf119936f8f1dc97b2b3e2f6 9356604 science optional relion_3.1.3-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
relion-dbgsym_3.1.3-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 329862800 bytes: control archive=3084 bytes.
2583 bytes, 12 lines control
5916 bytes, 56 lines md5sums
Package: relion-dbgsym
Source: relion
Version: 3.1.3-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 339163
Depends: relion (= 3.1.3-2)
Section: debug
Priority: optional
Description: debug symbols for relion
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lrwxrwxrwx root/root 0 2022-09-29 11:27 ./usr/share/doc/relion-dbgsym -> relion
relion-gui-dbgsym_3.1.3-2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 19908572 bytes: control archive=700 bytes.
462 bytes, 12 lines control
408 bytes, 4 lines md5sums
Package: relion-gui-dbgsym
Source: relion
Version: 3.1.3-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 20486
Depends: relion-gui (= 3.1.3-2)
Section: debug
Priority: optional
Description: debug symbols for relion-gui
Build-Ids: b484ce98a909f7665f94efda88f257ba2bc18eeb c1d7623aac70423acea9959fe3799992841d9fa2 c4c59be3ffe502947cf9984abf77120ac7a19195
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lrwxrwxrwx root/root 0 2022-09-29 11:27 ./usr/share/doc/relion-gui-dbgsym -> relion-gui
relion-gui_3.1.3-2_armhf.deb
----------------------------
new Debian package, version 2.0.
size 853076 bytes: control archive=1084 bytes.
1125 bytes, 22 lines control
387 bytes, 6 lines md5sums
Package: relion-gui
Source: relion
Version: 3.1.3-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4318
Depends: relion (= 3.1.3-2), libc6 (>= 2.34), libfftw3-double3 (>= 3.3.5), 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 2022-09-29 11:27 ./
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/bin/
-rwxr-xr-x root/root 2365228 2022-09-29 11:27 ./usr/bin/relion
-rwxr-xr-x root/root 1115920 2022-09-29 11:27 ./usr/bin/relion_display
-rwxr-xr-x root/root 919312 2022-09-29 11:27 ./usr/bin/relion_manualpick
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/share/
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/share/doc/relion-gui/
-rw-r--r-- root/root 1765 2022-09-29 11:27 ./usr/share/doc/relion-gui/changelog.Debian.gz
-rw-r--r-- root/root 7408 2022-09-29 11:27 ./usr/share/doc/relion-gui/copyright
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/share/lintian/
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 15 2022-09-29 11:27 ./usr/share/lintian/overrides/relion-gui
relion_3.1.3-2_armhf.deb
------------------------
new Debian package, version 2.0.
size 9356604 bytes: control archive=2636 bytes.
1146 bytes, 22 lines control
4218 bytes, 66 lines md5sums
Package: relion
Version: 3.1.3-2
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 (>= 3.3.5), libfftw3-single3 (>= 3.3.5), 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 2022-09-29 11:27 ./
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/bin/
-rwxr-xr-x root/root 788232 2022-09-29 11:27 ./usr/bin/relion_align_symmetry
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-rwxr-xr-x root/root 1705736 2022-09-29 11:27 ./usr/bin/relion_autopick_mpi
-rwxr-xr-x root/root 1246984 2022-09-29 11:27 ./usr/bin/relion_convert_star
-rwxr-xr-x root/root 919308 2022-09-29 11:27 ./usr/bin/relion_convert_to_tiff
-rwxr-xr-x root/root 919308 2022-09-29 11:27 ./usr/bin/relion_convert_to_tiff_mpi
-rwxr-xr-x root/root 1378060 2022-09-29 11:27 ./usr/bin/relion_ctf_mask_test
-rwxr-xr-x root/root 1967888 2022-09-29 11:27 ./usr/bin/relion_ctf_refine
-rwxr-xr-x root/root 1967888 2022-09-29 11:27 ./usr/bin/relion_ctf_refine_mpi
-rwxr-xr-x root/root 919304 2022-09-29 11:27 ./usr/bin/relion_ctf_toolbox
-rwxr-xr-x root/root 1312520 2022-09-29 11:27 ./usr/bin/relion_demodulate
-rwxr-xr-x root/root 722696 2022-09-29 11:27 ./usr/bin/relion_estimate_gain
-rwxr-xr-x root/root 919304 2022-09-29 11:27 ./usr/bin/relion_external_reconstruct
-rwxr-xr-x root/root 526088 2022-09-29 11:27 ./usr/bin/relion_find_tiltpairs
-rwxr-xr-x root/root 1967880 2022-09-29 11:27 ./usr/bin/relion_flex_analyse
-rwxr-xr-x root/root 1967880 2022-09-29 11:27 ./usr/bin/relion_flex_analyse_mpi
-rwxr-xr-x root/root 984840 2022-09-29 11:27 ./usr/bin/relion_helix_inimodel2d
-rwxr-xr-x root/root 1312520 2022-09-29 11:27 ./usr/bin/relion_helix_toolbox
-rwxr-xr-x root/root 1050376 2022-09-29 11:27 ./usr/bin/relion_image_handler
-rwxr-xr-x root/root 919304 2022-09-29 11:27 ./usr/bin/relion_import
-rwxr-xr-x root/root 1640200 2022-09-29 11:27 ./usr/bin/relion_localsym
-rwxr-xr-x root/root 1705736 2022-09-29 11:27 ./usr/bin/relion_localsym_mpi
-rwxr-xr-x root/root 1312520 2022-09-29 11:27 ./usr/bin/relion_mask_create
-rwxr-xr-x root/root 853772 2022-09-29 11:27 ./usr/bin/relion_merge_particles
-rwxr-xr-x root/root 2361120 2022-09-29 11:27 ./usr/bin/relion_motion_refine
-rwxr-xr-x root/root 2361120 2022-09-29 11:27 ./usr/bin/relion_motion_refine_mpi
-rwxr-xr-x root/root 657160 2022-09-29 11:27 ./usr/bin/relion_mrc2vtk
-rwxr-xr-x root/root 1574668 2022-09-29 11:27 ./usr/bin/relion_particle_FCC
-rwxr-xr-x root/root 2492168 2022-09-29 11:27 ./usr/bin/relion_particle_reposition
-rwxr-xr-x root/root 1246988 2022-09-29 11:27 ./usr/bin/relion_particle_select
-rwxr-xr-x root/root 2492172 2022-09-29 11:27 ./usr/bin/relion_particle_subtract
-rwxr-xr-x root/root 2492168 2022-09-29 11:27 ./usr/bin/relion_particle_subtract_mpi
-rwxr-xr-x root/root 984844 2022-09-29 11:27 ./usr/bin/relion_particle_symmetry_expand
-rwxr-xr-x root/root 1246984 2022-09-29 11:27 ./usr/bin/relion_pipeliner
-rwxr-xr-x root/root 1246984 2022-09-29 11:27 ./usr/bin/relion_plot_delocalisation
-rwxr-xr-x root/root 788236 2022-09-29 11:27 ./usr/bin/relion_postprocess
-rwxr-xr-x root/root 788236 2022-09-29 11:27 ./usr/bin/relion_postprocess_mpi
-rwxr-xr-x root/root 722696 2022-09-29 11:27 ./usr/bin/relion_prepare_subtomo
-rwxr-xr-x root/root 1312524 2022-09-29 11:27 ./usr/bin/relion_preprocess
-rwxr-xr-x root/root 1378060 2022-09-29 11:27 ./usr/bin/relion_preprocess_mpi
-rwxr-xr-x root/root 1902344 2022-09-29 11:27 ./usr/bin/relion_project
-rwxr-xr-x root/root 1902348 2022-09-29 11:27 ./usr/bin/relion_reconstruct
-rwxr-xr-x root/root 1967884 2022-09-29 11:27 ./usr/bin/relion_reconstruct_mpi
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-rwxr-xr-x root/root 2557704 2022-09-29 11:27 ./usr/bin/relion_refine_mpi
-rwxr-xr-x root/root 1574664 2022-09-29 11:27 ./usr/bin/relion_reposition
-rwxr-xr-x root/root 984840 2022-09-29 11:27 ./usr/bin/relion_run_ctffind
-rwxr-xr-x root/root 984840 2022-09-29 11:27 ./usr/bin/relion_run_ctffind_mpi
-rwxr-xr-x root/root 1246984 2022-09-29 11:27 ./usr/bin/relion_run_motioncorr
-rwxr-xr-x root/root 1246984 2022-09-29 11:27 ./usr/bin/relion_run_motioncorr_mpi
-rwxr-xr-x root/root 1771272 2022-09-29 11:27 ./usr/bin/relion_scheduler
-rwxr-xr-x root/root 919304 2022-09-29 11:27 ./usr/bin/relion_stack_create
-rwxr-xr-x root/root 1055 2022-09-29 11:27 ./usr/bin/relion_star_datablock_ctfdat
-rwxr-xr-x root/root 714 2022-09-29 11:27 ./usr/bin/relion_star_datablock_singlefiles
-rwxr-xr-x root/root 767 2022-09-29 11:27 ./usr/bin/relion_star_datablock_stack
-rwxr-xr-x root/root 984840 2022-09-29 11:27 ./usr/bin/relion_star_handler
-rwxr-xr-x root/root 675 2022-09-29 11:27 ./usr/bin/relion_star_loopheader
-rwxr-xr-x root/root 1217 2022-09-29 11:27 ./usr/bin/relion_star_plottable
-rwxr-xr-x root/root 2263 2022-09-29 11:27 ./usr/bin/relion_star_printtable
-rwxr-xr-x root/root 591624 2022-09-29 11:27 ./usr/bin/relion_tiltpair_plot
-rwxr-xr-x root/root 1246984 2022-09-29 11:27 ./usr/bin/relion_tomo_test
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/share/
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-09-29 11:27 ./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 1765 2022-09-29 11:27 ./usr/share/doc/relion/changelog.Debian.gz
-rw-r--r-- root/root 7408 2022-09-29 11:27 ./usr/share/doc/relion/copyright
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/share/lintian/
drwxr-xr-x root/root 0 2022-09-29 11:27 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 15 2022-09-29 11:27 ./usr/share/lintian/overrides/relion
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 4062044
Build-Time: 5620
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 1146
Job: relion_3.1.3-2
Machine Architecture: armhf
Package: relion
Package-Time: 6822
Source-Version: 3.1.3-2
Space: 4062044
Status: successful
Version: 3.1.3-2
--------------------------------------------------------------------------------
Finished at 2022-10-04T11:12:03Z
Build needed 01:53:42, 4062044k disc space