relion →
3.1.3-3+b1 →
armhf → 2023-01-14 20:17:35
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| relion 3.1.3-3+b1 (armhf) Sat, 14 Jan 2023 19:21:20 +0000 |
+==============================================================================+
Package: relion
Version: 3.1.3-3+b1
Source Version: 3.1.3-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-8f4296ec-bc85-447c-9203-64a6aba7836a' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/relion-Hj1tDY/resolver-LJfuku' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| 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 [13.6 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.4 MB]
Fetched 27.9 MB in 11s (2578 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'relion' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/relion.git
Please use:
git clone https://salsa.debian.org/med-team/relion.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2360 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main relion 3.1.3-3 (dsc) [2136 B]
Get:2 http://172.17.4.1/private bookworm-staging/main relion 3.1.3-3 (tar) [2345 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main relion 3.1.3-3 (diff) [12.0 kB]
Fetched 2360 kB in 0s (5430 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/relion-Hj1tDY/relion-3.1.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/relion-Hj1tDY' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid, build-essential, fakeroot
Filtered Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [405 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [488 B]
Fetched 1850 B in 0s (48.9 kB/s)
Reading package lists...
Reading package lists...
Install main 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
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-strip-nondeterminism dwz file fluid
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran-12
groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libarchive13 libbrotli1 libbsd0 libcairo2 libcbor0.8 libcurl4
libdebhelper-perl libdeflate-dev libdeflate0 libdrm-amdgpu1 libdrm-common
libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-2.1-7
libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3
libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1
libfreetype6 libgfortran-12-dev libgfortran5 libgl1 libgl1-mesa-dri
libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libhwloc-dev libhwloc-plugins
libhwloc15 libibverbs-dev libibverbs1 libicu72 libjbig-dev libjbig0
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libjs-jquery-ui
libjsoncpp25 liblerc-dev liblerc4 libllvm14 libltdl-dev libltdl7 liblzma-dev
libmagic-mgc libmagic1 libmd0 libmunge2 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 libproc2-0 libpsl5 libpthread-stubs0-dev
librdmacm1 librhash0 librtmp1 libsensors-config libsensors5 libssh2-1
libsub-override-perl libtiff-dev libtiff6 libtiffxx6 libtool libuchardet0
libuv1 libwebp-dev libwebp7 libwebpdemux2 libwebpmux3 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 libzstd-dev libzstd1 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 cmake-format
elpa-cmake-mode ninja-build 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
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-strip-nondeterminism dwz file fluid
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran-12
groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libarchive13 libbrotli1 libbsd0 libcairo2 libcbor0.8 libcurl4
libdebhelper-perl libdeflate-dev libdeflate0 libdrm-amdgpu1 libdrm-common
libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-2.1-7
libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3
libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1
libfreetype6 libgfortran-12-dev libgfortran5 libgl1 libgl1-mesa-dri
libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libhwloc-dev libhwloc-plugins
libhwloc15 libibverbs-dev libibverbs1 libicu72 libjbig-dev libjbig0
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libjs-jquery-ui
libjsoncpp25 liblerc-dev liblerc4 libllvm14 libltdl-dev libltdl7 liblzma-dev
libmagic-mgc libmagic1 libmd0 libmunge2 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 libproc2-0 libpsl5 libpthread-stubs0-dev
librdmacm1 librhash0 librtmp1 libsensors-config libsensors5 libssh2-1
libsub-override-perl libtiff-dev libtiff6 libtiffxx6 libtool libuchardet0
libuv1 libwebp-dev libwebp7 libwebpdemux2 libwebpmux3 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 libzstd-dev m4 man-db ocl-icd-libopencl1
openmpi-bin openmpi-common openssh-client po-debconf procps
sbuild-build-depends-main-dummy ucf x11proto-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
The following packages will be upgraded:
libzstd1
1 upgraded, 171 newly installed, 0 to remove and 45 not upgraded.
Need to get 89.8 MB of archives.
After this operation, 370 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libzstd1 armhf 1.5.2+dfsg2-3 [244 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libproc2-0 armhf 2:4.0.2-3 [53.6 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:4.0.2-3 [679 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 0.21-10 [156 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 0.11.7-1 [112 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20221030-2 [76.2 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 1.12.0-2 [67.6 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf openssh-client armhf 1:9.1p1-2 [811 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 1.4.19-2 [256 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 0.21-10 [495 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.6.2-1 [293 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 1.51.0-1 [60.5 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 7.87.0-1 [332 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 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 cmake-data all 3.25.1-1 [2026 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.25.1-1 [3859 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.4 [942 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.39-2 [258 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.3-3 [292 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.3-3 [687 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libxfixes3 armhf 1:6.0.0-2 [21.2 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libxcursor1 armhf 1:1.2.1-1 [38.0 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libxft2 armhf 2.3.6-1 [53.7 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libxinerama1 armhf 2:1.1.4-3 [17.4 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libfltk1.3 armhf 1.3.8-5+b1 [484 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libfltk-forms1.3 armhf 1.3.8-5+b1 [35.4 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libfltk-images1.3 armhf 1.3.8-5+b1 [46.7 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf fluid armhf 1.3.8-5+b1 [194 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-10+rpi1 [238 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-12-dev armhf 12.2.0-10+rpi1 [285 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf gfortran-12 armhf 12.2.0-10+rpi1 [7508 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.7.0-0.2 [55.0 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.2 [152 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libibverbs1 armhf 42.0-1 [53.7 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf ibverbs-providers armhf 42.0-1 [28.8 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.42.2-1 [461 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-7 [482 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.14-1 [48.1 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libdrm-common all 2.4.114-1+rpi1 [7276 B]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libdrm2 armhf 2.4.114-1+rpi1 [32.8 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libdrm-amdgpu1 armhf 2.4.114-1+rpi1 [19.3 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libdrm-nouveau2 armhf 2.4.114-1+rpi1 [17.0 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libdrm-radeon1 armhf 2.4.114-1+rpi1 [20.7 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-5+b1 [166 kB]
Get:94 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:95 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:96 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:97 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:98 http://172.17.4.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-5+b1 [280 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf librdmacm1 armhf 42.0-1 [60.3 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-3 [310 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-double3 armhf 3.3.10-1 [325 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-single3 armhf 3.3.10-1 [509 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-bin armhf 3.3.10-1 [40.8 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-dev armhf 3.3.10-1 [827 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libfltk-cairo1.3 armhf 1.3.8-5+b1 [29.8 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libglvnd0 armhf 1.5.0-1 [51.5 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libglapi-mesa armhf 22.2.0-1+rpi1 [84.6 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libx11-xcb1 armhf 2:1.8.3-3 [192 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libxcb-glx0 armhf 1.15-1 [121 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libxcb-present0 armhf 1.15-1 [105 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libxcb-sync1 armhf 1.15-1 [108 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf libxcb-xfixes0 armhf 1.15-1 [109 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libxshmfence1 armhf 1.3-1 [8636 B]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.1 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libz3-4 armhf 4.8.12-3 [5798 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libllvm14 armhf 1:14.0.6-9+rpi1 [19.5 MB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf libsensors5 armhf 1:3.6.0-7.1 [31.6 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libgl1-mesa-dri armhf 22.2.0-1+rpi1 [5593 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libglx-mesa0 armhf 22.2.0-1+rpi1 [171 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libglx0 armhf 1.5.0-1 [32.4 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libgl1 armhf 1.5.0-1 [91.8 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf libfltk-gl1.3 armhf 1.3.8-5+b1 [56.2 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf x11proto-dev all 2022.1-1 [599 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libxcb1-dev armhf 1.15-1 [175 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libx11-dev armhf 2:1.8.3-3 [768 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf libfltk1.3-dev armhf 1.3.8-5+b1 [790 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf libhwloc15 armhf 2.9.0-1 [124 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.16-1 [18.4 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.16-1 [31.5 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.7-5 [390 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.7-5 [161 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.9.0-1 [196 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.17-2 [48.8 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libxnvctrl0 armhf 510.108.03-1 [11.8 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.3 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.9.0-1 [16.0 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.7.0-0.2 [93.4 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.7.0-0.2 [163 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf libibverbs-dev armhf 42.0-1 [188 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-6.1 [27.0 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf libjbig-dev armhf 2.1-6.1 [27.2 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf liblerc4 armhf 4.0.0+ds-2 [133 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf liblerc-dev armhf 4.0.0+ds-2 [147 kB]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.4.0-0.1 [240 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf libmunge2 armhf 0.5.14-6 [18.6 kB]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf libpmix2 armhf 4.2.2-1 [530 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.4-3+rpi1 [1795 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf openmpi-common all 4.1.4-3+rpi1 [165 kB]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [901 kB]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf libpmix-dev armhf 4.2.2-1 [845 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.4-3+rpi1 [192 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.4-3+rpi1 [920 kB]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf libzstd-dev armhf 1.5.2+dfsg2-3 [301 kB]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2+b1 [237 kB]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf libwebpmux3 armhf 1.2.2-2+b1 [103 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf libwebpdemux2 armhf 1.2.2-2+b1 [95.5 kB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf libwebp-dev armhf 1.2.2-2+b1 [316 kB]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf libtiff6 armhf 4.5.0-3 [292 kB]
Get:171 http://172.17.4.1/private bookworm-staging/main armhf libtiffxx6 armhf 4.5.0-3 [144 kB]
Get:172 http://172.17.4.1/private bookworm-staging/main armhf libtiff-dev armhf 4.5.0-3 [414 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Preparing to unpack .../000-libuchardet0_0.0.7-1_armhf.deb ...
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Unpacking file (1:5.41-4) ...
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Unpacking gettext-base (0.21-10) ...
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Unpacking libmd0:armhf (1.0.4-2) ...
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Unpacking libbsd0:armhf (0.11.7-1) ...
Selecting previously unselected package libedit2:armhf.
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Unpacking libedit2:armhf (3.1-20221030-2) ...
Selecting previously unselected package libcbor0.8:armhf.
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Unpacking libcbor0.8:armhf (0.8.0-2) ...
Selecting previously unselected package libfido2-1:armhf.
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Unpacking libfido2-1:armhf (1.12.0-2) ...
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Unpacking openssh-client (1:9.1p1-2) ...
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Moving old data out of the way
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Unpacking m4 (1.4.19-2) ...
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Selecting previously unselected package libicu72:armhf.
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Unpacking libicu72:armhf (72.1-3) ...
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Unpacking libxml2:armhf (2.9.14+dfsg-1.1) ...
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Unpacking libarchive13:armhf (3.6.2-1) ...
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
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Selecting previously unselected package libxrender1:armhf.
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Unpacking libxft2:armhf (2.3.6-1) ...
Selecting previously unselected package libxinerama1:armhf.
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Selecting previously unselected package libfltk1.3:armhf.
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Unpacking libfltk1.3:armhf (1.3.8-5+b1) ...
Selecting previously unselected package libfltk-forms1.3:armhf.
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Unpacking libfltk-forms1.3:armhf (1.3.8-5+b1) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
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Setting up libmunge2 (0.5.14-6) ...
Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
Setting up libx11-data (2:1.8.3-3) ...
Setting up libjpeg62-turbo-dev:armhf (1:2.1.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libproc2-0:armhf (2:4.0.2-3) ...
Setting up libpng16-16:armhf (1.6.39-2) ...
Setting up libhwloc15:armhf (2.9.0-1) ...
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 (0.21-10) ...
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 (1:3.6.0-7.1) ...
Setting up liblerc-dev:armhf (4.0.0+ds-2) ...
Setting up libltdl7:armhf (2.4.7-5) ...
Setting up libfftw3-double3:armhf (3.3.10-1) ...
Setting up libglapi-mesa:armhf (22.2.0-1+rpi1) ...
Setting up libgfortran5:armhf (12.2.0-10+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up libwebp7:armhf (1.2.2-2+b1) ...
Setting up liblzma-dev:armhf (5.4.0-0.1) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ...
Setting up libnuma1:armhf (2.0.16-1) ...
Setting up libmd0:armhf (1.0.4-2) ...
Setting up ocl-icd-libopencl1:armhf (2.3.1-1) ...
Setting up libxshmfence1:armhf (1.3-1) ...
Setting up librhash0:armhf (1.4.3-3) ...
Setting up libtiff6:armhf (4.5.0-3) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up procps (2:4.0.2-3) ...
Setting up libnl-3-200:armhf (3.7.0-0.2) ...
Setting up openmpi-common (4.1.4-3+rpi1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up xorg-sgml-doctools (1:1.11-1.1) ...
Setting up cmake-data (3.25.1-1) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libfido2-1:armhf (1.12.0-2) ...
Setting up libwebpmux3:armhf (1.2.2-2+b1) ...
Setting up libbsd0:armhf (0.11.7-1) ...
Setting up libtiffxx6:armhf (4.5.0-3) ...
Setting up libdeflate-dev:armhf (1.14-1) ...
Setting up libdrm-common (2.4.114-1+rpi1) ...
Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.1) ...
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 (1.13.0-2) ...
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 (0.21-10) ...
Setting up libxcb-xfixes0:armhf (1.15-1) ...
Setting up libtool (2.4.7-5) ...
Setting up libarchive13:armhf (3.6.2-1) ...
Setting up libxcb-render0:armhf (1.15-1) ...
Setting up libfftw3-bin (3.3.10-1) ...
Setting up fontconfig-config (2.13.1-4.5) ...
Setting up libxcb-glx0:armhf (1.15-1) ...
Setting up libwebpdemux2:armhf (1.2.2-2+b1) ...
Setting up libedit2:armhf (3.1-20221030-2) ...
Setting up libjpeg-dev:armhf (1:2.1.2-1) ...
Setting up libjbig-dev:armhf (2.1-6.1) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-5+b1) ...
Setting up libgfortran-12-dev:armhf (12.2.0-10+rpi1) ...
Setting up libxcb-shm0:armhf (1.15-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnuma-dev:armhf (2.0.16-1) ...
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 (2.4.7-5) ...
Setting up gfortran-12 (12.2.0-10+rpi1) ...
Setting up libwebp-dev:armhf (1.2.2-2+b1) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libfreetype6:armhf (2.12.1+dfsg-3) ...
Setting up libtiff-dev:armhf (4.5.0-3) ...
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 (1.13.0-2) ...
Setting up libllvm14:armhf (1:14.0.6-9+rpi1) ...
Setting up libdrm2:armhf (2.4.114-1+rpi1) ...
Setting up dwz (0.15-1) ...
Setting up libnl-3-dev:armhf (3.7.0-0.2) ...
Setting up groff-base (1.22.4-9) ...
Setting up libcurl4:armhf (7.87.0-1) ...
Setting up libx11-6:armhf (2:1.8.3-3) ...
Setting up libhwloc-dev:armhf (2.9.0-1) ...
Setting up libfftw3-dev:armhf (3.3.10-1) ...
Setting up libdrm-amdgpu1:armhf (2.4.114-1+rpi1) ...
Setting up libxcb-dri3-0:armhf (1.15-1) ...
Setting up libx11-xcb1:armhf (2:1.8.3-3) ...
Setting up libibverbs1:armhf (42.0-1) ...
Setting up libdrm-nouveau2:armhf (2.4.114-1+rpi1) ...
Setting up libxrender1:armhf (1:0.9.10-1.1) ...
Setting up ibverbs-providers:armhf (42.0-1) ...
Setting up libdrm-radeon1:armhf (2.4.114-1+rpi1) ...
Setting up openssh-client (1:9.1p1-2) ...
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 (2.11.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ...
Setting up libxnvctrl0:armhf (510.108.03-1) ...
Setting up libnl-route-3-dev:armhf (3.7.0-0.2) ...
Setting up libxfixes3:armhf (1:6.0.0-2) ...
Setting up libxinerama1:armhf (2:1.1.4-3) ...
Setting up cmake (3.25.1-1) ...
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 (13.11.4) ...
Setting up libibverbs-dev:armhf (42.0-1) ...
Setting up libhwloc-plugins:armhf (2.9.0-1) ...
Setting up libgl1:armhf (1.5.0-1) ...
Setting up libfabric1:armhf (1.11.0-3) ...
Setting up libpmix2:armhf (4.2.2-1) ...
Setting up libopenmpi3:armhf (4.1.4-3+rpi1) ...
Setting up libpmix-dev:armhf (4.2.2-1) ...
Setting up openmpi-bin (4.1.4-3+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.1.4-3+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Processing triggers for libc-bin (2.36-6+rpi1) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Setting up x11proto-dev (2022.1-1) ...
Setting up libxft2:armhf (2.3.6-1) ...
Setting up libxau-dev:armhf (1:1.0.9-1) ...
Setting up libfltk1.3:armhf (1.3.8-5+b1) ...
Setting up libfltk-gl1.3:armhf (1.3.8-5+b1) ...
Setting up libfltk-images1.3:armhf (1.3.8-5+b1) ...
Setting up libcairo2:armhf (1.16.0-7) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up libfltk-forms1.3:armhf (1.3.8-5+b1) ...
Setting up libxcb1-dev:armhf (1.15-1) ...
Setting up libx11-dev:armhf (2:1.8.3-3) ...
Setting up libfltk-cairo1.3:armhf (1.3.8-5+b1) ...
Setting up fluid (1.3.8-5+b1) ...
Setting up libfltk1.3-dev:armhf (1.3.8-5+b1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.36-6+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39.50.20221208-5+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-10+rpi1 gcc-12_12.2.0-10+rpi1 libc6-dev_2.36-6+rpi1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 linux-libc-dev_6.0.12-1+rpi1
Package versions: adduser_3.129 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2-2 binutils_2.39.50.20221208-5+rpi1 binutils-arm-linux-gnueabihf_2.39.50.20221208-5+rpi1 binutils-common_2.39.50.20221208-5+rpi1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b2 cmake_3.25.1-1 cmake-data_3.25.1-1 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.80 debhelper_13.11.4 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dirmngr_2.2.40-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 fluid_1.3.8-5+b1 fontconfig-config_2.13.1-4.5 fonts-dejavu-core_2.37-2 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-10+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-10+rpi1 gcc-12-base_12.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-10 gettext-base_0.21-10 gfortran-12_12.2.0-10+rpi1 gnupg_2.2.40-1 gnupg-l10n_2.2.40-1 gnupg-utils_2.2.40-1 gpg_2.2.40-1 gpg-agent_2.2.40-1 gpg-wks-client_2.2.40-1 gpg-wks-server_2.2.40-1 gpgconf_2.2.40-1 gpgsm_2.2.40-1 gpgv_2.2.40-1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1 hostname_3.23 ibverbs-providers_42.0-1 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-1 libacl1_2.3.1-2 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libarchive13_3.6.2-1 libasan8_12.2.0-10+rpi1 libassuan0_2.5.5-5 libatomic1_12.2.0-10+rpi1 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39.50.20221208-5+rpi1 libblkid1_2.38.1-4 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-6+rpi1 libc-dev-bin_2.36-6+rpi1 libc6_2.36-6+rpi1 libc6-dev_2.36-6+rpi1 libcairo2_1.16.0-7 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_12.2.0-10+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libctf-nobfd0_2.39.50.20221208-5+rpi1 libctf0_2.39.50.20221208-5+rpi1 libcurl4_7.87.0-1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.265 libdebhelper-perl_13.11.4 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdpkg-perl_1.21.9+rpi1 libdrm-amdgpu1_2.4.114-1+rpi1 libdrm-common_2.4.114-1+rpi1 libdrm-nouveau2_2.4.114-1+rpi1 libdrm-radeon1_2.4.114-1+rpi1 libdrm2_2.4.114-1+rpi1 libedit2_3.1-20221030-2 libelf1_0.187-2+rpi2 libevent-2.1-7_2.1.12-stable-5+b1 libevent-core-2.1-7_2.1.12-stable-5+b1 libevent-dev_2.1.12-stable-5+b1 libevent-extra-2.1-7_2.1.12-stable-5+b1 libevent-openssl-2.1-7_2.1.12-stable-5+b1 libevent-pthreads-2.1-7_2.1.12-stable-5+b1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfabric1_1.11.0-3 libfakeroot_1.29-1 libffi8_3.4.4-1 libfftw3-bin_3.3.10-1 libfftw3-dev_3.3.10-1 libfftw3-double3_3.3.10-1 libfftw3-single3_3.3.10-1 libfido2-1_1.12.0-2 libfile-stripnondeterminism-perl_1.13.0-2 libfltk-cairo1.3_1.3.8-5+b1 libfltk-forms1.3_1.3.8-5+b1 libfltk-gl1.3_1.3.8-5+b1 libfltk-images1.3_1.3.8-5+b1 libfltk1.3_1.3.8-5+b1 libfltk1.3-dev_1.3.8-5+b1 libfontconfig1_2.13.1-4.5 libfreetype6_2.12.1+dfsg-3 libgcc-12-dev_12.2.0-10+rpi1 libgcc-s1_12.2.0-10+rpi1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.2.0-10+rpi1 libgfortran5_12.2.0-10+rpi1 libgl1_1.5.0-1 libgl1-mesa-dri_22.2.0-1+rpi1 libglapi-mesa_22.2.0-1+rpi1 libglvnd0_1.5.0-1 libglx-mesa0_22.2.0-1+rpi1 libglx0_1.5.0-1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-4 libgomp1_12.2.0-10+rpi1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-1 libhogweed6_3.8.1-2 libhwloc-dev_2.9.0-1 libhwloc-plugins_2.9.0-1 libhwloc15_2.9.0-1 libibverbs-dev_42.0-1 libibverbs1_42.0-1 libicu72_72.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjansson4_2.14-2 libjbig-dev_2.1-6.1 libjbig0_2.1-6.1 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_1.20.1-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 libksba8_1.6.2-4 libldap-2.5-0_2.5.13+dfsg-2+rpi1+b1 liblerc-dev_4.0.0+ds-2 liblerc4_4.0.0+ds-2 libllvm14_1:14.0.6-9+rpi1 libltdl-dev_2.4.7-5 libltdl7_2.4.7-5 liblz4-1_1.9.4-1+rpi1 liblzma-dev_5.4.0-0.1 liblzma5_5.4.0-0.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-4 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libmunge2_0.5.14-6 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.51.0-1 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_2.0.16-1 libnuma1_2.0.16-1 libopenmpi-dev_4.1.4-3+rpi1 libopenmpi3_4.1.4-3+rpi1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpciaccess0_0.17-2 libpcre2-8-0_10.40-3 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.36_5.36.0-6 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpmix-dev_4.2.2-1 libpmix2_4.2.2-1 libpng16-16_1.6.39-2 libproc2-0_2:4.0.2-3 libpsl5_0.21.0-1.2 libpthread-stubs0-dev_0.4-1 librdmacm1_42.0-1 libreadline8_8.2-1.2 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsensors-config_1:3.6.0-7.1 libsensors5_1:3.6.0-7.1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-4 libsqlite3-0_3.40.0-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.2-1+rpi1 libtasn1-6_4.19.0-2 libtiff-dev_4.5.0-3 libtiff6_4.5.0-3 libtiffxx6_4.5.0-3 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libubsan1_12.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_252.2-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-4 libuv1_1.44.2-1+rpi1 libwebp-dev_1.2.2-2+b1 libwebp7_1.2.2-2+b1 libwebpdemux2_1.2.2-2+b1 libwebpmux3_1.2.2-2+b1 libx11-6_2:1.8.3-3 libx11-data_2:1.8.3-3 libx11-dev_2:1.8.3-3 libx11-xcb1_2:1.8.3-3 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb-dri2-0_1.15-1 libxcb-dri3-0_1.15-1 libxcb-glx0_1.15-1 libxcb-present0_1.15-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb-sync1_1.15-1 libxcb-xfixes0_1.15-1 libxcb1_1.15-1 libxcb1-dev_1.15-1 libxcursor1_1:1.2.1-1 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxfixes3_1:6.0.0-2 libxft2_2.3.6-1 libxinerama1_2:1.1.4-3 libxml2_2.9.14+dfsg-1.1 libxnvctrl0_510.108.03-1 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_4.8.12-3 libzstd-dev_1.5.2+dfsg2-3 libzstd1_1.5.2+dfsg2-3 linux-libc-dev_6.0.12-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-2 make_4.3-4.1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-4 nano_7.1-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 ocl-icd-libopencl1_2.3.1-1 openmpi-bin_4.1.4-3+rpi1 openmpi-common_4.1.4-3+rpi1 openssh-client_1:9.1p1-2 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-6 perl-base_5.36.0-6 perl-modules-5.32_5.32.1-6 perl-modules-5.36_5.36.0-6 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 procps_2:4.0.2-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.2 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-7 tar_1.34+dfsg-1 tzdata_2022f-1 ucf_3.0043 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 x11proto-dev_2022.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.4.0-0.1 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: relion
Binary: relion, relion-gui
Architecture: any
Version: 3.1.3-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Roland Fehrenbacher <rfehren@debian.org>, Andreas Tille <tille@debian.org>,
Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/relion
Vcs-Git: https://salsa.debian.org/med-team/relion.git
Testsuite: autopkgtest
Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid
Package-List:
relion deb science optional arch=any
relion-gui deb science optional arch=any
Checksums-Sha1:
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cedf552f19f9220b11446223278ef4b6df384211 11968 relion_3.1.3-3.debian.tar.xz
Checksums-Sha256:
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936e23f8684572278e88c2461490e05cb5fa970589243496e6e19f9daae29831 11968 relion_3.1.3-3.debian.tar.xz
Files:
5ddaf9afe51d743c5f58f625d9fd1cb7 2345487 relion_3.1.3.orig.tar.gz
88162835b2d24fc130241c8131f0adbe 11968 relion_3.1.3-3.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.CaxPYpxo/trustedkeys.kbx': General error
gpgv: Signature made Tue Dec 6 11:51:10 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./relion_3.1.3-3.dsc
dpkg-source: info: extracting relion in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking relion_3.1.3.orig.tar.gz
dpkg-source: info: unpacking relion_3.1.3-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch
dpkg-source: info: applying typos.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 3.1.3-3+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=f6531457acff44088f965ef4ced20cd2
JOURNAL_STREAM=8:31902
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-8f4296ec-bc85-447c-9203-64a6aba7836a
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c56523
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package relion
dpkg-buildpackage: info: source version 3.1.3-3+b1
dpkg-buildpackage: info: source distribution bookworm-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -rf build
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir /<<PKGBUILDDIR>>/build
cd /<<PKGBUILDDIR>>/build; \
CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON -DGUI=ON -DCUDA=OFF /<<PKGBUILDDIR>>
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
CMake Warning (dev) at /usr/share/cmake-3.25/Modules/CMakeDetermineCompilerId.cmake:93 (if):
Policy CMP0054 is not set: Only interpret if() arguments as variables or
keywords when unquoted. Run "cmake --help-policy CMP0054" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.
Quoted variables like "CUDA" will no longer be dereferenced when the policy
is set to NEW. Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
/usr/share/cmake-3.25/Modules/CMakeDetermineCCompiler.cmake:123 (CMAKE_DETERMINE_COMPILER_ID)
CMakeLists.txt:6 (project)
This warning is for project developers. Use -Wno-dev to suppress it.
-- The C compiler identification is GNU 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- Detecting C compiler ABI info
CMake Warning (dev) at /usr/share/cmake-3.25/Modules/CMakeDetermineCompilerABI.cmake:29 (if):
Policy CMP0054 is not set: Only interpret if() arguments as variables or
keywords when unquoted. Run "cmake --help-policy CMP0054" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.
Quoted variables like "CUDA" will no longer be dereferenced when the policy
is set to NEW. Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
/usr/share/cmake-3.25/Modules/CMakeTestCCompiler.cmake:26 (CMAKE_DETERMINE_COMPILER_ABI)
CMakeLists.txt:6 (project)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- BUILD TYPE set to the default type: 'Release'
-- Setting fallback CUDA_ARCH=35
-- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2
-- Setting cpu precision to double
-- Setting accelerated code precision to single
-- Using non-cuda compilation....
-- Found MPI_C: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- MPI_INCLUDE_PATH : /usr/lib/arm-linux-gnueabihf/openmpi/include;/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi
-- MPI_LIBRARIES : /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so
-- MPI_CXX_INCLUDE_PATH : /usr/lib/arm-linux-gnueabihf/openmpi/include;/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi
-- MPI_CXX_LIBRARIES : /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so
-- CMAKE_C_COMPILER : /usr/bin/gcc
-- CMAKE_CXX_COMPILER : /usr/bin/g++
-- MPI_C_COMPILER : /usr/bin/mpicc
-- MPI_CXX_COMPILER : /usr/bin/mpicxx
-- CMAKE_CXX_COMPILER_ID : GNU
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Found FLTK: fltk_images;fltk_forms;fltk
-- X11 and FLTK were found
-- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/arm-linux-gnueabihf/libX11.so;/usr/lib/arm-linux-gnueabihf/libm.so
-- Found FFTW
-- FFTW_PATH: /usr/include
-- FFTW_INCLUDES: /usr/include
-- FFTW_LIBRARIES: /usr/lib/arm-linux-gnueabihf/libfftw3f.so;/usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for sincos
-- Looking for sincos - found
-- Looking for __sincos
-- Looking for __sincos - not found
-- Found TIFF: /usr/lib/arm-linux-gnueabihf/libtiff.so (found version "4.5.0")
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.13")
-- 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
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_plottable /<<PKGBUILDDIR>>/build/bin/relion_star_plottable
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 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/__/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/__/__/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/__/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/assembly.h:15,
from /<<PKGBUILDDIR>>/src/assembly.cpp:8:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Atom&}; _Tp = Atom; _Alloc = std::allocator<Atom>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Atom>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’,
inlined from ‘long int Residue::addAtom(std::string, double, double, double, double, double)’ at /<<PKGBUILDDIR>>/src/assembly.cpp:36:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Atom*, std::vector<Atom> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’:
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/CPlot2D.h:30,
from /<<PKGBUILDDIR>>/src/CPlot2D.cpp:27:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<CDataPoint>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35,
inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/vector.tcc:232:44:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<CDataSet>::iterator’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, std::vector<Residue> >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*; _Tp = Residue]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Molecule::Molecule(const Molecule&)’ at /<<PKGBUILDDIR>>/src/assembly.h:118:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Molecule; _Args = {const Molecule&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const Molecule*; _ForwardIterator = Molecule*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const Residue*; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In 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 static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Residue&}; _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/vector.tcc:462:28:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(std::vector<double>, std::vector<double>)’ at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:505:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void CPlot2D::AddDataSet(int, double*, double*)’ at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:478:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(int, double*, double*)’ at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:480:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30,
inlined from ‘void Assembly::sortResidues()’ at /<<PKGBUILDDIR>>/src/assembly.cpp:487:26:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {Residue&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = Residue*; _ForwardIterator = Residue*; _Tp = Residue]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/vector.tcc:251:35,
inlined from ‘void Assembly::sortResidues()’ at /<<PKGBUILDDIR>>/src/assembly.cpp:489:30:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void CPlot2D::AddDataSet(std::vector<double>)’ at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:523:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(std::vector<double>)’ at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:525:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/autopicker_mpi.cpp
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30,
inlined from ‘long int Molecule::addResidue(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); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/CPlot2D.cpp: In member function ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)’:
/<<PKGBUILDDIR>>/src/CPlot2D.cpp:743:41: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac);
| ^~
/<<PKGBUILDDIR>>/src/CPlot2D.cpp:743:37: note: directive argument in the range [0, 2147483647]
743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /<<PKGBUILDDIR>>/src/CPlot2D.cpp:21:
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)’ at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:743:16:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 14 bytes into a destination of size 10
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/CPlot2D.cpp: In member function ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)’:
/<<PKGBUILDDIR>>/src/CPlot2D.cpp:733:41: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac);
| ^~
/<<PKGBUILDDIR>>/src/CPlot2D.cpp:733:37: note: directive argument in the range [0, 2147483647]
733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac);
| ^~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)’ at /<<PKGBUILDDIR>>/src/CPlot2D.cpp:733:16:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 14 bytes into a destination of size 10
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, std::vector<Residue> >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*; _Tp = Residue]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Molecule::Molecule(const Molecule&)’ at /<<PKGBUILDDIR>>/src/assembly.h:118:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::_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 static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, std::vector<Residue> >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*; _Tp = Residue]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Molecule::Molecule(const Molecule&)’ at /<<PKGBUILDDIR>>/src/assembly.h:118:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Molecule; _Alloc = std::allocator<Molecule>]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30,
inlined from ‘long int Assembly::addMolecule(std::string, std::string)’ at /<<PKGBUILDDIR>>/src/assembly.cpp:131:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /<<PKGBUILDDIR>>/src/backprojector.cpp
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/vector.tcc:145:30:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘std::vector<_Tp, _Alloc>::_Temporary_value::_Temporary_value(std::vector<_Tp, _Alloc>*, _Args&& ...) [with _Args = {const Residue&}; _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/stl_vector.h:1830:30,
inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/vector.tcc:156:23:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {Residue}; _Tp = Residue]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {Residue}; _Tp = Residue]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(iterator, _Arg&&) [with _Arg = Residue; _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/vector.tcc:417:31,
inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/vector.tcc:157:19:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30,
inlined from ‘long int Molecule::addResidue(Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.cpp:57:20,
inlined from ‘void Molecule::insertResidues(Molecule, int, int)’ at /<<PKGBUILDDIR>>/src/assembly.cpp:116:14:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, std::vector<Residue> >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*; _Tp = Residue]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Molecule::Molecule(const Molecule&)’ at /<<PKGBUILDDIR>>/src/assembly.h:118:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Molecule; _Alloc = std::allocator<Molecule>]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30,
inlined from ‘long int Assembly::addMolecule(Molecule&)’ at /<<PKGBUILDDIR>>/src/assembly.cpp:162:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/autopicker.h:10,
from /<<PKGBUILDDIR>>/src/autopicker_mpi.h:12,
from /<<PKGBUILDDIR>>/src/autopicker_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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 /<<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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
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,
| ^~~~~~~~~~~~~
/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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
/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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/__/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
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 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:1809:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<ccfPeak*, vector<ccfPeak> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:1809:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:1856:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:1924:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:1929:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:1964:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:2035:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:2104:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:2174:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:2218:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:2219:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:2221:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator<ccfPeak>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:2275:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ccfPeak*, std::vector<ccfPeak> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void AutoPicker::extractHelicalTubes(std::vector<ccfPeak>&, std::vector<std::vector<ccfPeak> >&, std::vector<double, std::allocator<double> >&, std::vector<std::vector<ccfPeak> >&, double, double, double, double, float)’ at /<<PKGBUILDDIR>>/src/autopicker.cpp:2293:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/funcs.h:56:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<CDataPoint>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<CDataSet>::iterator’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /<<PKGBUILDDIR>>/src/helix.cpp
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/Healpix_2.15a/healpix_base.h:35,
from /<<PKGBUILDDIR>>/src/healpix_sampling.h:24:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:417:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:420:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:421:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:425:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:426:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:436:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:437:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::addOneTranslation(double, double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:469:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::addOneTranslation(double, double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:470:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::addOneTranslation(double, double, double, bool, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:472:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1923:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1924:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1925:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1933:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1934:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1937:50:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::getOrientations(long int, long int, int, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1844:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::getOrientations(long int, long int, int, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1845:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::getOrientations(long int, long int, int, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1846:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/helix.h:30,
from /<<PKGBUILDDIR>>/src/helix.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::findSymmetryMate(long int, double, std::vector<int>&, std::vector<double>&, std::vector<bool>&)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1096:29:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::removePointsOutsideLimitedTiltAngles()’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:2101:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::removePointsOutsideLimitedTiltAngles()’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:2102:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1758:34:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1759:34:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1760:34:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1765:33:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1766:33:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::addOneOrientation(double, double, double, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:572:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::addOneOrientation(double, double, double, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:573:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::addOneOrientation(double, double, double, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:578:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::addOneOrientation(double, double, double, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:579:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::addOneOrientation(double, double, double, bool)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:584:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1365:31:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1381:30:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1397:29:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1436:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:1469:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:846:31:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:922:31:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:938:29:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:968:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector<int>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, double, double, double)’ at /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:992:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp
In file included from /<<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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:564:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:567:13:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:567:13:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In 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/algorithm:61,
from /<<PKGBUILDDIR>>/src/funcs.h:55,
from /<<PKGBUILDDIR>>/src/multidim_array.h:52,
from /<<PKGBUILDDIR>>/src/helix.h:26:
/usr/include/c++/12/bits/stl_algo.h: In function ‘_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >]’:
/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
1281 | __rotate(_RandomAccessIterator __first,
| ^~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:471:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:472:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:473:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:474:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(CDataSet)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:476:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:509:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:512:13:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:512:13:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:535:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:536:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:537:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:538:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(CDataSet)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
inlined from ‘void FlexAnalyser::makePCAhistograms(std::vector<std::vector<double, std::allocator<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/flex_analyser.cpp:544:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -MF CMakeFiles/relion_lib.dir/__/image.cpp.o.d -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /<<PKGBUILDDIR>>/src/image.cpp
/usr/include/c++/12/bits/stl_algo.h: In function ‘_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = HelicalSegmentPriorInfoEntry*; _OutputIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2615 | __move_merge(_InputIterator __first1, _InputIterator __last1,
| ^~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _OutputIterator = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2682 | __merge_sort_with_buffer(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
In function ‘void std::__chunk_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2693:34:
/usr/include/c++/12/bits/stl_algo.h:2672:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2672 | std::__insertion_sort(__first, __first + __chunk_size, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2675 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
In function ‘void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _RandomAccessIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2697:26:
/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2650 | __result = std::__move_merge(__first, __first + __step_size,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2651 | __first + __step_size,
| ~~~~~~~~~~~~~~~~~~~~~~
2652 | __first + __two_step,
| ~~~~~~~~~~~~~~~~~~~~~
2653 | __result, __comp);
| ~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2658 | std::__move_merge(__first, __first + __step_size,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2659 | __first + __step_size, __last, __result, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
In function ‘void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = HelicalSegmentPriorInfoEntry*; _RandomAccessIterator2 = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2700:26:
/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2650 | __result = std::__move_merge(__first, __first + __step_size,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2651 | __first + __step_size,
| ~~~~~~~~~~~~~~~~~~~~~~
2652 | __first + __two_step,
| ~~~~~~~~~~~~~~~~~~~~~
2653 | __result, __comp);
| ~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2658 | std::__move_merge(__first, __first + __step_size,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2659 | __first + __step_size, __last, __result, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /<<PKGBUILDDIR>>/src/local_symmetry.cpp
In file included from /<<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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/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 /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 /<<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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
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 /<<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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/funcs.h:56:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:4957:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:4958:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:4959:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void 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>::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 member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2051:61:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2052:61:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2053:62:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2054:62:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2055:71:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2056:56:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2057:75:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2058:69:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2059:56:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2060:65:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2062:60:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2064:69:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2066:66:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2068:70:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)’ at /<<PKGBUILDDIR>>/src/helix.cpp:2070:71:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void 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>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>::
| ^~~~~~~~~~~~~~~~~~~
[ 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
/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
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:5283:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:5293:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:5295:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:5305:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:5307:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:5334:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:5335:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)’ at /<<PKGBUILDDIR>>/src/helix.cpp:5336:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -MF CMakeFiles/relion_lib.dir/__/memory.cpp.o.d -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /<<PKGBUILDDIR>>/src/memory.cpp
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /<<PKGBUILDDIR>>/src/metadata_container.cpp
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /<<PKGBUILDDIR>>/src/metadata_label.cpp
/usr/include/c++/12/bits/stl_algo.h: In function ‘_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _BidirectionalIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int]’:
/usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2352 | __rotate_adaptive(_BidirectionalIterator1 __first,
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
In function ‘_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >]’,
inlined from ‘_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _BidirectionalIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int]’ at /usr/include/c++/12/bits/stl_algo.h:2383:20:
/usr/include/c++/12/bits/stl_algo.h:1397:27: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
1397 | return std::__rotate(__first, __middle, __last,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
1398 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2390 | __merge_adaptive(_BidirectionalIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2435:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2435 | = std::__rotate_adaptive(__first_cut, __middle, __second_cut,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2436 | __len1 - __len11, __len22, __buffer,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2437 | __buffer_size);
| ~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2438:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2438 | std::__merge_adaptive(__first, __first_cut, __new_middle, __len11,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2439 | __len22, __buffer, __buffer_size, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2440:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2440 | std::__merge_adaptive(__new_middle, __second_cut, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2441 | __len1 - __len11,
| ~~~~~~~~~~~~~~~~~
2442 | __len2 - __len22, __buffer,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2443 | __buffer_size, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Pointer = HelicalSegmentPriorInfoEntry*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:2709:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2709 | __stable_sort_adaptive(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2709:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2718:38: note: parameter passing for argument of type ‘const __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2718 | std::__stable_sort_adaptive(__first, __middle, __buffer,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2719 | __buffer_size, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2720:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2720 | std::__stable_sort_adaptive(__middle, __last, __buffer,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
2721 | __buffer_size, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2725:40: note: parameter passing for argument of type ‘const __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2725 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2726:40: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2726 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2729:28: note: parameter passing for argument of type ‘const __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2729 | std::__merge_adaptive(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2730 | _Distance(__middle - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2731 | _Distance(__last - __middle),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2732 | __buffer, __buffer_size,
| ~~~~~~~~~~~~~~~~~~~~~~~~
2733 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:2451:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2451 | __merge_without_buffer(_BidirectionalIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2451:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2451:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
In function ‘_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >]’,
inlined from ‘void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2491:15:
/usr/include/c++/12/bits/stl_algo.h:1397:27: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
1397 | return std::__rotate(__first, __middle, __last,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
1398 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:2492:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2492 | std::__merge_without_buffer(__first, __first_cut, __new_middle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2493 | __len11, __len22, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2494:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2494 | std::__merge_without_buffer(__new_middle, __second_cut, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2495 | __len1 - __len11, __len2 - __len22, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:2739:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2739 | __inplace_stable_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2739:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2748 | std::__inplace_stable_sort(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2749 | std::__inplace_stable_sort(__middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2748 | std::__inplace_stable_sort(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2748 | std::__inplace_stable_sort(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2749 | std::__inplace_stable_sort(__middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2748 | std::__inplace_stable_sort(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2749 | std::__inplace_stable_sort(__middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2748 | std::__inplace_stable_sort(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2749 | std::__inplace_stable_sort(__middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2748 | std::__inplace_stable_sort(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2749 | std::__inplace_stable_sort(__middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2748 | std::__inplace_stable_sort(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2749 | std::__inplace_stable_sort(__middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2748:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2748 | std::__inplace_stable_sort(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2749 | std::__inplace_stable_sort(__middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2744 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2748 | std::__inplace_stable_sort(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2749 | std::__inplace_stable_sort(__middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2749:33:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
2750 | std::__merge_without_buffer(__first, __middle, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2751 | __middle - __first,
| ~~~~~~~~~~~~~~~~~~~
2752 | __last - __middle,
| ~~~~~~~~~~~~~~~~~~
2753 | __comp);
| ~~~~~~~
/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>::
| ^~~~~~~~~~~~~~~~~~~
[ 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
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = HelicalSegmentPriorInfoEntry; _Alloc = std::allocator<HelicalSegmentPriorInfoEntry>]’,
inlined from ‘void updatePriorsForHelicalReconstruction(MetaDataTable&, double, std::vector<double, std::allocator<double> >, std::vector<double, std::allocator<double> >, int, bool, bool, double, double, double, double, bool, int)’ at /<<PKGBUILDDIR>>/src/helix.cpp:4475:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, vector<HelicalSegmentPriorInfoEntry> >]’ at /usr/include/c++/12/bits/stl_algo.h:5034:36,
inlined from ‘void updatePriorsForHelicalReconstruction(MetaDataTable&, double, std::vector<double, std::allocator<double> >, std::vector<double, std::allocator<double> >, int, bool, bool, double, double, double, double, bool, int)’ at /<<PKGBUILDDIR>>/src/helix.cpp:4479:18:
/usr/include/c++/12/bits/stl_algo.h:4996:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
4996 | _TmpBuf __buf(__first, (__last - __first + 1) / 2);
| ^~~~~
/usr/include/c++/12/bits/stl_algo.h:4999:35: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
4999 | std::__inplace_stable_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:5001:36: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HelicalSegmentPriorInfoEntry*, std::vector<HelicalSegmentPriorInfoEntry> >’ changed in GCC 7.1
5001 | std::__stable_sort_adaptive(__first, __last, __buf.begin(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5002 | _DistanceType(__buf.size()), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’:
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35,
inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/vector.tcc:232:44:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Residue*, vector<Residue> >; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Atom*, vector<Atom> >; _ForwardIterator = Atom*; _Tp = Atom]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator<Atom>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘Residue::Residue(const Residue&)’ at /<<PKGBUILDDIR>>/src/assembly.h:73:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {Residue&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = Residue*; _ForwardIterator = Residue*; _Tp = Residue]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator<Residue>]’ at /usr/include/c++/12/bits/vector.tcc:251:35:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Atom*, std::vector<Atom> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1550:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1553:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1557:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1560:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1564:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1567:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1577:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1580:16:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1585:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1588:16:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1593:17:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void getLocalSearchOperatorSamplings(const Matrix1D<double>&, const Matrix1D<double>&, std::vector<Matrix1D<double> >&, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/local_symmetry.cpp:1596:16:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from /<<PKGBUILDDIR>>/src/funcs.h:55,
from /<<PKGBUILDDIR>>/src/metadata_table.h:43,
from /<<PKGBUILDDIR>>/src/metadata_table.cpp:45:
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Distance = int; _Tp = pair<double, long int>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /<<PKGBUILDDIR>>/src/micrograph_model.cpp
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/metadata_table.h:33:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<CDataPoint>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<CDataSet>::iterator’ changed in GCC 7.1
In file included from /<<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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1528:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(CDataSet)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
inlined from ‘void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1532:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1363:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1363:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1407:14:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1408:14:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘static void MetaDataTable::histogram(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, std::string, CPlot2D*, long int, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1363:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MetaDataTable::columnHistogram(EMDLabel, std::vector<double>&, std::vector<double>&, int, CPlot2D*, long int, double, double, bool, bool)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:1341:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<double, long int>}; _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::pair<double, long int> >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, long int>}; _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void MetaDataTable::sort(EMDLabel, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:508:15:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void MetaDataTable::sort(EMDLabel, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:512:11:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int> > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void MetaDataTable::sort(EMDLabel, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:512:11:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int> > >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘bool MetaDataTable::setValueFromString(EMDLabel, const std::string&, long int)’ at /<<PKGBUILDDIR>>/src/metadata_table.cpp:385:16:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/micrograph_model.h:23,
from /<<PKGBUILDDIR>>/src/micrograph_model.cpp:21:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In 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 ‘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 member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Micrograph::setMovie(FileName, FileName, double)’ at /<<PKGBUILDDIR>>/src/micrograph_model.cpp:575:21:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void Micrograph::setMovie(FileName, FileName, double)’ at /<<PKGBUILDDIR>>/src/micrograph_model.cpp:576:21:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/projector.h:25,
from /<<PKGBUILDDIR>>/src/ml_model.h:23,
from /<<PKGBUILDDIR>>/src/ml_model.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /<<PKGBUILDDIR>>/src/ml_optimiser.cpp
[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/projector.h:25,
from /<<PKGBUILDDIR>>/src/ml_model.h:23,
from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
from /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:44:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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/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/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 member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlModel::initialiseBodies(FileName, FileName, bool, int)’ at /<<PKGBUILDDIR>>/src/ml_model.cpp:1085:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlModel::initialiseBodies(FileName, FileName, bool, int)’ at /<<PKGBUILDDIR>>/src/ml_model.cpp:1086:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlModel::initialiseBodies(FileName, FileName, bool, int)’ at /<<PKGBUILDDIR>>/src/ml_model.cpp:1087:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlModel::initialiseBodies(FileName, FileName, bool, int)’ at /<<PKGBUILDDIR>>/src/ml_model.cpp:1088:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlModel::initialise(bool)’ at /<<PKGBUILDDIR>>/src/ml_model.cpp:45:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In 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 file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/ml_optimiser.h:33:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator<BackProjector>]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<BackProjector>::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<BackProjector*>; _ForwardIterator = BackProjector*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<BackProjector*>; _ForwardIterator = BackProjector*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<BackProjector*>; _ForwardIterator = BackProjector*; _Tp = BackProjector]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = BackProjector*; _ForwardIterator = BackProjector*; _Allocator = allocator<BackProjector>]’ at /usr/include/c++/12/bits/stl_uninitialized.h:382:41,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator<BackProjector>]’ at /usr/include/c++/12/bits/vector.tcc:542:32:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘std::move_iterator<BackProjector*>’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<BackProjector*>; _ForwardIterator = BackProjector*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<BackProjector*>; _ForwardIterator = BackProjector*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<BackProjector*>; _ForwardIterator = BackProjector*; _Tp = BackProjector]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = BackProjector*; _ForwardIterator = BackProjector*; _Allocator = allocator<BackProjector>]’ at /usr/include/c++/12/bits/stl_uninitialized.h:382:41,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator<BackProjector>]’ at /usr/include/c++/12/bits/vector.tcc:562:32:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘std::move_iterator<BackProjector*>’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator<BackProjector>]’,
inlined from ‘void MlWsumModel::initialise(MlModel&, FileName, bool, bool)’ at /<<PKGBUILDDIR>>/src/ml_model.cpp:1503:14:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BackProjector*, std::vector<BackProjector> >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void MlOptimiser::maximizationOtherParameters()’ at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:4255:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void MlOptimiser::maximizationOtherParameters()’ at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:4255:12:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[ 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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
[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /<<PKGBUILDDIR>>/src/pipeline_control.cpp
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlOptimiser::initialiseGeneral(int)’ at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:1933:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlOptimiser::initialiseGeneral(int)’ at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:1934:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlOptimiser::initialiseGeneral(int)’ at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:1938:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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 ‘void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray<double>&, MultidimArray<bool>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<Matrix1D<double> >&, std::vector<Matrix1D<double> >&, std::vector<double, std::allocator<double> >&, std::vector<int>&, std::vector<int>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:6682:23:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray<double>&, MultidimArray<bool>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<Matrix1D<double> >&, std::vector<Matrix1D<double> >&, std::vector<double, std::allocator<double> >&, std::vector<int>&, std::vector<int>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’ at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:7049:31:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector: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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /<<PKGBUILDDIR>>/src/pipeliner.cpp
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void MlOptimiser::expectationOneParticle(long int, int)’ at /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:3741:32:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /<<PKGBUILDDIR>>/src/postprocessing.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/postprocessing.h:24,
from /<<PKGBUILDDIR>>/src/postprocessing.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/funcs.h:56,
from /<<PKGBUILDDIR>>/src/image.h:58:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const fit_point2D&}; _Tp = fit_point2D; _Alloc = std::allocator<fit_point2D>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<fit_point2D>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fit_point2D; _Alloc = std::allocator<fit_point2D>]’,
inlined from ‘void Postprocessing::makeGuinierPlot(MultidimArray<tComplex<double> >&, std::vector<fit_point2D>&)’ at /<<PKGBUILDDIR>>/src/postprocessing.cpp:652:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<fit_point2D*, std::vector<fit_point2D> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /<<PKGBUILDDIR>>/src/preprocessing.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
from /<<PKGBUILDDIR>>/src/preprocessing.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
from /<<PKGBUILDDIR>>/src/scheduler.h:26,
from /<<PKGBUILDDIR>>/src/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/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
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>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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:61:
/usr/include/c++/12/bits/stl_map.h: In function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]’:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]’,
inlined from ‘float Schedule::getFloatVariableValue(std::string)’ at /<<PKGBUILDDIR>>/src/scheduler.cpp:1080:37:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]’,
inlined from ‘float Schedule::getFloatOriginalVariableValue(std::string)’ at /<<PKGBUILDDIR>>/src/scheduler.cpp:1087:37:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]’,
inlined from ‘void Schedule::setFloatOriginalVariableValue(std::string, double)’ at /<<PKGBUILDDIR>>/src/scheduler.cpp:1102:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]’,
inlined from ‘void Schedule::addFloatVariable(std::string, double)’ at /<<PKGBUILDDIR>>/src/scheduler.cpp:1055:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]’,
inlined from ‘void Schedule::setFloatVariableValue(std::string, double)’ at /<<PKGBUILDDIR>>/src/scheduler.cpp:1094:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = SchedulerFloatVariable; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >]’,
inlined from ‘void Schedule::setFloatVariableValue(std::string, double)’ at /<<PKGBUILDDIR>>/src/scheduler.cpp:1095:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, SchedulerFloatVariable> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/time.h:31,
from /<<PKGBUILDDIR>>/src/scheduler.h:24:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<double, long int>}; _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, long int>}; _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<double, long int>; _Alloc = std::allocator<std::pair<double, long int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void MultidimArray<T>::sorted_index(MultidimArray<long int>&) const [with T = double]’ at /<<PKGBUILDDIR>>/src/multidim_array.h:3618:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void MultidimArray<T>::sorted_index(MultidimArray<long int>&) const [with T = double]’ at /<<PKGBUILDDIR>>/src/multidim_array.h:3621:18:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, long int>*, vector<pair<double, long int>, allocator<pair<double, long int> > > >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void MultidimArray<T>::sorted_index(MultidimArray<long int>&) const [with T = double]’ at /<<PKGBUILDDIR>>/src/multidim_array.h:3621:18:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, long int>*, std::vector<std::pair<double, long int>, std::allocator<std::pair<double, long int> > > >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/tiff_converter.cpp:24:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::estimate(FileName)’:
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:141:101: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=]
141 | printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n",
| ~~~^
| |
| int
| %10ld
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:141:108: warning: format ‘%d’ expects argument of type ‘int’, but argument 8 has type ‘long int’ [-Wformat=]
141 | printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n",
| ~~~^
| |
| int
| %10ld
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function ‘int TIFFConverter::checkMRCtype(FileName)’:
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:309:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
309 | fread(headers, sizeof(int), 24, mrcin);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::initialise(int, int)’:
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:367:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
367 | system(("mkdir -p " + fn_out.beforeLastOf("/")).c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::run()’:
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:530:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
530 | system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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
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<>());
| ~~~~~~~~~~~~~~~
[ 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::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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/convolution_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/complex_io.h:24,
from /<<PKGBUILDDIR>>/src/jaz/complex_io.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/convolution_helper.h:24,
from /<<PKGBUILDDIR>>/src/jaz/convolution_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -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
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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_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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
from /<<PKGBUILDDIR>>/src/ctf.h:50,
from /<<PKGBUILDDIR>>/src/jaz/fsc_helper.h:24,
from /<<PKGBUILDDIR>>/src/jaz/damage_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/distribution_helper.cpp
[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/fftw_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/distribution_helper.h:25,
from /<<PKGBUILDDIR>>/src/jaz/distribution_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/image_log.cpp
[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/interpolation.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/image_log.h:24,
from /<<PKGBUILDDIR>>/src/jaz/image_log.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/interpolation.h:24,
from /<<PKGBUILDDIR>>/src/jaz/interpolation.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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
[ 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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
[ 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
[ 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/gradient_descent.cpp
[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/lbfgs.cpp
[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/nelder_mead.cpp
[ 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
[ 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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.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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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 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>::
| ^~~~~~~~~~~~~~~~~~~
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<int, gravis::t2Vector<double> >}; _Tp = std::pair<int, gravis::t2Vector<double> >; _Alloc = std::allocator<std::pair<int, gravis::t2Vector<double> > >]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::pair<int, gravis::t2Vector<double> > >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<int, gravis::t2Vector<double> >}; _Tp = std::pair<int, gravis::t2Vector<double> >; _Alloc = std::allocator<std::pair<int, gravis::t2Vector<double> > >]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<int, gravis::t2Vector<double> >; _Alloc = std::allocator<std::pair<int, gravis::t2Vector<double> > >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘_ZN14BFactorRefiner17processMicrographElR13MetaDataTableRKSt6vectorI5ImageI8tComplexIdEESaIS6_EESA_b._omp_fn.1’ at /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:237:36:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<int, gravis::t2Vector<double> >*, std::vector<std::pair<int, gravis::t2Vector<double> > > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 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 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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 /<<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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void DefocusEstimator::writeEPS(const MetaDataTable&)’ at /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.cpp:218:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(CDataSet)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
inlined from ‘void DefocusEstimator::writeEPS(const MetaDataTable&)’ at /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.cpp:220:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/equation2x2.cpp
[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.cpp
[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_helper.cpp
[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/modular_ctf_optimisation.cpp
[ 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
from /<<PKGBUILDDIR>>/src/ctf.h:50,
from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_helper.h:24,
from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/ctf/modular_ctf_optimisation.h:5,
from /<<PKGBUILDDIR>>/src/jaz/ctf/modular_ctf_optimisation.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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 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 /<<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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/funcs.h:56,
from /<<PKGBUILDDIR>>/src/multidim_array.h:52,
from /<<PKGBUILDDIR>>/src/ctf.h:48:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘static void TiltHelper::extractTilt(std::vector<double, std::allocator<double> >&, double&, double&, double, double)’ at /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.cpp:536:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘static void TiltHelper::insertTilt(std::vector<double, std::allocator<double> >&, double, double, double, double)’ at /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.cpp:563:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
from /<<PKGBUILDDIR>>/src/ctf.h:50,
from /<<PKGBUILDDIR>>/src/jaz/motion/motion_helper.h:24,
from /<<PKGBUILDDIR>>/src/jaz/motion/motion_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/three_hyperparameter_fit.cpp
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)’ at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:711:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(CDataSet)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
inlined from ‘void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)’ at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:714:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)’ at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:724:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(CDataSet)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
inlined from ‘void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)’ at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:725:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)’ at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:736:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(CDataSet)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
inlined from ‘void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)’ at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:737:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator<CDataPoint>]’,
inlined from ‘void CDataSet::AddDataPoint(CDataPoint)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:168:33,
inlined from ‘void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)’ at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:751:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataPoint*, std::vector<CDataPoint> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator<CDataSet>]’,
inlined from ‘void CPlot2D::AddDataSet(CDataSet)’ at /<<PKGBUILDDIR>>/src/CPlot2D.h:1198:26,
inlined from ‘void MotionEstimator::writeOutput(const std::vector<std::vector<gravis::t2Vector<double> > >&, double, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<Image<double> >&, const std::vector<gravis::t2Vector<double> >&, std::string, double)’ at /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:753:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CDataSet*, std::vector<CDataSet> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/two_hyperparameter_fit.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/motion/alignment_set.h:24,
from /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.h:24,
from /<<PKGBUILDDIR>>/src/jaz/motion/three_hyperparameter_fit.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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
[ 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/img_proc/image_op.cpp
[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/backprojection_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/img_proc/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/imod_helper.cpp
[ 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/io/star_converter.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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>::
| ^~~~~~~~~~~~~~~~~~~
/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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
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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.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/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
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /<<PKGBUILDDIR>>/src/displayer.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/autopicker.h:10,
from /<<PKGBUILDDIR>>/src/apps/autopick.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/projector.h:25,
from /<<PKGBUILDDIR>>/src/apps/align_symmetry.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 54%] Linking CXX executable ../../bin/relion_autopick
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
[ 55%] Linking CXX executable ../../bin/relion_autopick_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 55%] Built target autopick
/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 55%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -MF CMakeFiles/convert_star.dir/convert_star.cpp.o.d -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /<<PKGBUILDDIR>>/src/apps/convert_star.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 55%] Built target autopick_mpi
/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'
[ 55%] 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 55%] 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
[ 56%] 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'
[ 56%] Built target convert_to_tiff
/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 57%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 57%] Built target convert_star
/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'
[ 57%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 57%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 57%] 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'
[ 57%] 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
[ 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
/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'
[ 57%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 58%] 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'
[ 58%] 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'
[ 59%] 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
[ 59%] 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
[ 60%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 60%] Built target ctf_refine_mpi
/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'
[ 60%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 60%] 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'
[ 60%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /<<PKGBUILDDIR>>/src/apps/estimate_gain.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 61%] 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
[ 61%] Linking CXX executable ../../bin/relion_ctf_toolbox
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 61%] Built target ctf_toolbox
/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'
[ 62%] 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
[ 62%] 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
[ 63%] 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'
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/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'
[ 63%] 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
[ 63%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 63%] 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'
[ 63%] 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 64%] 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
[ 65%] 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
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/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=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 65%] 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'
[ 65%] Built target find_tiltpairs
/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'
[ 66%] 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
[ 66%] Linking CXX executable ../../bin/relion_external_reconstruct
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target external_reconstruct
/usr/bin/make -f src/apps/CMakeFiles/helix_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'
[ 67%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 67%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 67%] 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'
[ 67%] 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
[ 67%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 67%] 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'
[ 67%] Built target flex_analyse_mpi
/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'
[ 67%] 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 67%] 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'
[ 67%] Built target import
/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 68%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 68%] 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'
[ 68%] 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'
[ 69%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/localsym_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/local_symmetry.h:30,
from /<<PKGBUILDDIR>>/src/local_symmetry_mpi.h:5,
from /<<PKGBUILDDIR>>/src/apps/localsym_mpi.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 69%] 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
[ 69%] 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
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/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
[ 69%] Built target helix_toolbox
/usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 69%] 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'
[ 69%] Built target localsym_mpi
/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'
[ 70%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 71%] 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
[ 72%] 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
[ 72%] 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
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/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
[ 72%] Built target image_handler
/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'
[ 73%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 73%] Built target merge_particles
/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'
[ 73%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/motion_refine_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
from /<<PKGBUILDDIR>>/src/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 73%] 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
[ 74%] 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
[ 74%] 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/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
/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'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 74%] 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=
[ 74%] Built target mask_create
/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
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'
[ 74%] 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
[ 75%] 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'
[ 75%] Built target motion_refine_mpi
/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'
[ 76%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 76%] 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
[ 76%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 76%] Built target particle_FCC
/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'
[ 76%] 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
[ 76%] 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'
[ 76%] Built target mrc2vtk
/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'
[ 76%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 77%] 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'
[ 77%] Built target particle_select
/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'
[ 78%] 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
[ 78%] 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 78%] 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'
[ 78%] Built target relion_gui_lib
/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'
[ 79%] 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
[ 80%] Linking CXX executable ../../bin/relion_particle_subtract
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 80%] 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'
[ 80%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 80%] Linking CXX executable ../../bin/relion_particle_reposition
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
[ 80%] 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'
[ 80%] Built target particle_symmetry_expand
/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'
[ 80%] 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
[ 80%] 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'
[ 80%] Built target particle_reposition
/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'
[ 80%] 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
[ 81%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 81%] Built target particle_subtract_mpi
/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'
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'
[ 81%] Built target pipeliner
/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend
[ 82%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.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/prepare_subtomo.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/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'
/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'
[ 82%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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_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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 82%] 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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target postprocess
/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 82%] 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
[ 82%] 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'
[ 82%] Built target postprocess_mpi
/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend
[ 83%] 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
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=
/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'
/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'
[ 83%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target plot_delocalisation
/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'
[ 84%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /<<PKGBUILDDIR>>/src/apps/project.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
from /<<PKGBUILDDIR>>/src/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 85%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target preprocess
/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 85%] 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 /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
[ 85%] Linking CXX executable ../../bin/relion_preprocess_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] 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'
[ 85%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 86%] 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
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 86%] 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'
[ 86%] 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
[ 87%] 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'
[ 87%] 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'
[ 88%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
from /<<PKGBUILDDIR>>/src/projector.h:25,
from /<<PKGBUILDDIR>>/src/ml_model.h:23,
from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
from /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.h:24,
from /<<PKGBUILDDIR>>/src/apps/refine_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31,
from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 88%] 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
[ 88%] 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'
[ 88%] Built target project
/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'
[ 88%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /<<PKGBUILDDIR>>/src/apps/reposition.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] Built target refine
/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'
/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'
[ 88%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /<<PKGBUILDDIR>>/src/apps/run_ctffind.cpp
[ 88%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] 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
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 89%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 90%] 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
[ 90%] 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'
[ 90%] Built target prepare_subtomo
/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 91%] 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
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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target run_ctffind
/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'
[ 91%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 91%] Linking CXX executable ../../bin/relion_run_ctffind_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target run_ctffind_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=
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'
[ 91%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 91%] 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
[ 92%] 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'
[ 92%] Built target run_motioncorr
/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'
[ 93%] 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
[ 94%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 94%] Built target reposition
/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'
[ 95%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /<<PKGBUILDDIR>>/src/apps/star_handler.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 95%] 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'
[ 95%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 96%] 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
[ 96%] 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'
[ 96%] 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'
[ 96%] 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 96%] Built target scheduler
/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'
[ 96%] 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/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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 97%] Linking CXX executable ../../bin/relion_display
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff
In file included from /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>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 97%] Built target display
/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'
[ 97%] 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 /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>::
| ^~~~~~~~~~~~~~~~~~~
[ 97%] 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'
[ 97%] Built target stack_create
/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'
[ 97%] 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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
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 /<<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:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
[ 98%] Linking CXX executable ../../bin/relion_tomo_test
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void star_handler_parameters::discard_on_image_stats()’ at /<<PKGBUILDDIR>>/src/apps/star_handler.cpp:292:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void star_handler_parameters::discard_on_image_stats()’ at /<<PKGBUILDDIR>>/src/apps/star_handler.cpp:293:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 99%] 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'
[ 99%] Built target tomo_test
[100%] Linking CXX executable ../../bin/relion_manualpick
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target manualpick
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target relion
[100%] Linking CXX executable ../../bin/relion_star_handler
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/star_handler.dir/star_handler.cpp.o -o ../../bin/relion_star_handler ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target star_handler
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -C build install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp/cli
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
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_printtable /<<PKGBUILDDIR>>/build/bin/relion_star_printtable
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_plottable /<<PKGBUILDDIR>>/build/bin/relion_star_plottable
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_loopheader /<<PKGBUILDDIR>>/build/bin/relion_star_loopheader
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_stack /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_stack
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_singlefiles /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_singlefiles
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_ctfdat /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_ctfdat
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/qsub.csh /<<PKGBUILDDIR>>/build/bin/relion_qsub.csh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 0%] Built target copy_scripts
/usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_lib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 53%] Built target relion_lib
/usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_gui_lib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 56%] Built target relion_gui_lib
/usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/align_symmetry.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 56%] Built target align_symmetry
/usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 57%] Built target autopick
/usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 58%] Built target autopick_mpi
/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_star.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 59%] Built target convert_star
/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 59%] Built target convert_to_tiff
/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 60%] Built target convert_to_tiff_mpi
/usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_mask_test.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 61%] Built target ctf_mask_test
/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 62%] Built target ctf_refine
/usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 62%] Built target ctf_refine_mpi
/usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_toolbox.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 63%] Built target ctf_toolbox
/usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/demodulate.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 64%] Built target demodulate
/usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/display.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 65%] Built target display
/usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/estimate_gain.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 65%] Built target estimate_gain
/usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/external_reconstruct.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target external_reconstruct
/usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/find_tiltpairs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 67%] Built target find_tiltpairs
/usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 68%] Built target flex_analyse
/usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 68%] Built target flex_analyse_mpi
/usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_inimodel2d.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 69%] Built target helix_inimodel2d
/usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_toolbox.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 70%] Built target helix_toolbox
/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/image_handler.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 71%] Built target image_handler
/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/import.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 71%] Built target import
/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 72%] Built target localsym
/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 73%] Built target localsym_mpi
/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 74%] Built target relion
/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/manualpick.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 75%] Built target manualpick
/usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/mask_create.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 75%] Built target mask_create
/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/merge_particles.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 76%] Built target merge_particles
/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 77%] Built target motion_refine
/usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 78%] Built target motion_refine_mpi
/usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/mrc2vtk.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 78%] Built target mrc2vtk
/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_FCC.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 79%] Built target particle_FCC
/usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_reposition.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 80%] Built target particle_reposition
/usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_select.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 81%] Built target particle_select
/usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target particle_subtract
/usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target particle_subtract_mpi
/usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_symmetry_expand.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target particle_symmetry_expand
/usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/pipeliner.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 84%] Built target pipeliner
/usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/plot_delocalisation.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target plot_delocalisation
/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target postprocess
/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 86%] Built target postprocess_mpi
/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/prepare_subtomo.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 87%] Built target prepare_subtomo
/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] Built target preprocess
/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] Built target preprocess_mpi
/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/project.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 89%] Built target project
/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 90%] Built target reconstruct
/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color=
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'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target reconstruct_mpi
/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target refine
/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color=
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/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'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 92%] Built target refine_mpi
/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/reposition.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 93%] Built target reposition
/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color=
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'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 93%] Built target run_ctffind
/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color=
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'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 94%] Built target run_ctffind_mpi
/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color=
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/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'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr.dir/build'.
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[ 95%] Built target run_motioncorr
/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color=
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'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 96%] Built target run_motioncorr_mpi
/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: 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=
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'
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=
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'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/star_handler.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 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=
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'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/tiltpair_plot.dir/build'.
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'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/tomo_test.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target tomo_test
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
make[3]: Nothing to be done for 'preinstall'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_star
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_align_symmetry
-- 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_ctf_toolbox
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_estimate_gain
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_demodulate
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_find_tiltpairs
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_external_reconstruct
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_import
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_toolbox
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_image_handler
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_merge_particles
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mask_create
-- 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_reposition
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_pipeliner
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_plot_delocalisation
-- 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_project
-- 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_prepare_subtomo
-- 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_run_motioncorr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reposition
-- 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_display
-- 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
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_manualpick
-- 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_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-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-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 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/relion-gui/usr/bin/relion_display debian/relion-gui/usr/bin/relion_manualpick debian/relion-gui/usr/bin/relion were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_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_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_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_particle_reposition contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_helix_toolbox contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_pipeliner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_import contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_ctffind 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_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_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_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_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_ctf_refine 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_particle_subtract_mpi debian/relion/usr/bin/relion_ctf_refine_mpi debian/relion/usr/bin/relion_particle_subtract debian/relion/usr/bin/relion_motion_refine_mpi debian/relion/usr/bin/relion_particle_reposition debian/relion/usr/bin/relion_helix_toolbox debian/relion/usr/bin/relion_preprocess debian/relion/usr/bin/relion_autopick_mpi debian/relion/usr/bin/relion_flex_analyse debian/relion/usr/bin/relion_tiltpair_plot debian/relion/usr/bin/relion_merge_particles debian/relion/usr/bin/relion_run_motioncorr_mpi debian/relion/usr/bin/relion_reconstruct_mpi debian/relion/usr/bin/relion_convert_to_tiff debian/relion/usr/bin/relion_particle_FCC debian/relion/usr/bin/relion_image_handler debian/relion/usr/bin/relion_scheduler debian/relion/usr/bin/relion_ctf_mask_test debian/relion/usr/bin/relion_motion_refine debian/relion/usr/bin/relion_reposition debian/relion/usr/bin/relion_mask_create debian/relion/usr/bin/relion_project debian/relion/usr/bin/relion_prepare_subtomo debian/relion/usr/bin/relion_stack_create debian/relion/usr/bin/relion_pipeliner debian/relion/usr/bin/relion_refine_mpi debian/relion/usr/bin/relion_localsym debian/relion/usr/bin/relion_run_ctffind_mpi debian/relion/usr/bin/relion_localsym_mpi debian/relion/usr/bin/relion_external_reconstruct debian/relion/usr/bin/relion_star_handler debian/relion/usr/bin/relion_convert_to_tiff_mpi debian/relion/usr/bin/relion_particle_select debian/relion/usr/bin/relion_align_symmetry debian/relion/usr/bin/relion_particle_symmetry_expand debian/relion/usr/bin/relion_mrc2vtk debian/relion/usr/bin/relion_convert_star debian/relion/usr/bin/relion_autopick debian/relion/usr/bin/relion_postprocess debian/relion/usr/bin/relion_reconstruct debian/relion/usr/bin/relion_run_motioncorr debian/relion/usr/bin/relion_tomo_test debian/relion/usr/bin/relion_plot_delocalisation debian/relion/usr/bin/relion_helix_inimodel2d debian/relion/usr/bin/relion_refine debian/relion/usr/bin/relion_demodulate debian/relion/usr/bin/relion_ctf_toolbox debian/relion/usr/bin/relion_import debian/relion/usr/bin/relion_run_ctffind debian/relion/usr/bin/relion_estimate_gain debian/relion/usr/bin/relion_find_tiltpairs debian/relion/usr/bin/relion_flex_analyse_mpi debian/relion/usr/bin/relion_preprocess_mpi debian/relion/usr/bin/relion_postprocess_mpi debian/relion/usr/bin/relion_ctf_refine were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'relion' in '../relion_3.1.3-3+b1_armhf.deb'.
dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3+b1_armhf.deb'.
dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.3-3+b1_armhf.deb'.
dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.3-3+b1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../relion_3.1.3-3+b1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../relion_3.1.3-3+b1_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 2023-01-14T20:16:42Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
relion_3.1.3-3+b1_armhf.changes:
--------------------------------
Format: 1.8
Date: Sat, 14 Jan 2023 19:38:08 +0000
Source: relion (3.1.3-3)
Binary: relion relion-dbgsym relion-gui relion-gui-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 3.1.3-3+b1
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Raspbian pi4 based autobuilder <root@raspbian.org>
Description:
relion - toolkit for 3D reconstructions in cryo-electron microscopy
relion-gui - toolkit for 3D reconstructions in cryo-electron microscopy (gui a
Changes:
relion (3.1.3-3+b1) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
4ea790123a1c821b92c906f4117a97bd999f044e 329863708 relion-dbgsym_3.1.3-3+b1_armhf.deb
f0015e085d032afb9ea9efd510294103ee0018eb 19902676 relion-gui-dbgsym_3.1.3-3+b1_armhf.deb
1fd788363d71dfe9f8e381a97da9a89acc203724 851776 relion-gui_3.1.3-3+b1_armhf.deb
30c7f0f7fb9b598e9169a32cc57c0e4c15d4d5f2 10457 relion_3.1.3-3+b1_armhf.buildinfo
b592fc7252f471a2d7c00b1e731928ef429f4c18 9362604 relion_3.1.3-3+b1_armhf.deb
Checksums-Sha256:
72dffac7e7a867314a9fb60981ec522999d1947b837e8e05e65275b33b4b2b4d 329863708 relion-dbgsym_3.1.3-3+b1_armhf.deb
fa6075804296e61564d5ccff5cb56a279ccdfe6725ec90ffd034cd7e1c2ab8b9 19902676 relion-gui-dbgsym_3.1.3-3+b1_armhf.deb
1d8c42f2447e5b1dbb37e754a71a7bb960b56d0d2bc7dfbaaeed56167332e3d9 851776 relion-gui_3.1.3-3+b1_armhf.deb
8276c23b31e2cac43c4baf22d4135e0be095dd4b6cc87c3a1bfce9bed87b1fa7 10457 relion_3.1.3-3+b1_armhf.buildinfo
14ece9d9687281696f5c70705c9c5efff7577c6e563416da72e8e0787854003e 9362604 relion_3.1.3-3+b1_armhf.deb
Files:
f08b4d6861f407cb75705c577157fca6 329863708 debug optional relion-dbgsym_3.1.3-3+b1_armhf.deb
7fbdc1d1c5b198ae9d6df8416ee65597 19902676 debug optional relion-gui-dbgsym_3.1.3-3+b1_armhf.deb
56ad5f15f9956a906ce67c5d2ba1d829 851776 science optional relion-gui_3.1.3-3+b1_armhf.deb
48232bad1f86d2b5a772f9288c0fcfe6 10457 science optional relion_3.1.3-3+b1_armhf.buildinfo
4399ec7d87412bb077e71946ecb98688 9362604 science optional relion_3.1.3-3+b1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: relion (3.1.3-3)
Binary: relion relion-dbgsym relion-gui relion-gui-dbgsym
Architecture: armhf
Version: 3.1.3-3+b1
Binary-Only-Changes:
relion (3.1.3-3+b1) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi4 based autobuilder <root@raspbian.org> Sat, 14 Jan 2023 19:38:08 +0000
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Checksums-Sha256:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 14 Jan 2023 20:16:32 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
adduser (= 3.129),
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-10),
autotools-dev (= 20220109.1),
base-files (= 12.3+rpi1),
base-passwd (= 3.6.1),
bash (= 5.2-2),
binutils (= 2.39.50.20221208-5+rpi1),
binutils-arm-linux-gnueabihf (= 2.39.50.20221208-5+rpi1),
binutils-common (= 2.39.50.20221208-5+rpi1),
bsdextrautils (= 2.38.1-4),
bsdutils (= 1:2.38.1-4),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
cmake (= 3.25.1-1),
cmake-data (= 3.25.1-1),
coreutils (= 9.1-1),
cpp (= 4:12.2.0-1+rpi1),
cpp-12 (= 12.2.0-10+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-9),
debconf (= 1.5.80),
debhelper (= 13.11.4),
debianutils (= 5.7-0.4),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.0-2),
diffutils (= 1:3.8-1),
dpkg (= 1.21.9+rpi1),
dpkg-dev (= 1.21.9+rpi1),
dwz (= 0.15-1),
file (= 1:5.41-4),
findutils (= 4.9.0-3),
fluid (= 1.3.8-5+b1),
fontconfig-config (= 2.13.1-4.5),
fonts-dejavu-core (= 2.37-2),
g++ (= 4:12.2.0-1+rpi1),
g++-12 (= 12.2.0-10+rpi1),
gcc (= 4:12.2.0-1+rpi1),
gcc-12 (= 12.2.0-10+rpi1),
gcc-12-base (= 12.2.0-10+rpi1),
gettext (= 0.21-10),
gettext-base (= 0.21-10),
gfortran-12 (= 12.2.0-10+rpi1),
grep (= 3.8-3),
groff-base (= 1.22.4-9),
gzip (= 1.12-1),
hostname (= 3.23),
ibverbs-providers (= 42.0-1),
init-system-helpers (= 1.64),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-2),
libarchive-zip-perl (= 1.68-1),
libarchive13 (= 3.6.2-1),
libasan8 (= 12.2.0-10+rpi1),
libatomic1 (= 12.2.0-10+rpi1),
libattr1 (= 1:2.5.1-3),
libaudit-common (= 1:3.0.7-1.1),
libaudit1 (= 1:3.0.7-1.1),
libbinutils (= 2.39.50.20221208-5+rpi1),
libblkid1 (= 2.38.1-4),
libbrotli1 (= 1.0.9-2+b2),
libbsd0 (= 0.11.7-1),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.36-6+rpi1),
libc-dev-bin (= 2.36-6+rpi1),
libc6 (= 2.36-6+rpi1),
libc6-dev (= 2.36-6+rpi1),
libcairo2 (= 1.16.0-7),
libcap-ng0 (= 0.8.3-1),
libcap2 (= 1:2.44-1),
libcbor0.8 (= 0.8.0-2),
libcc1-0 (= 12.2.0-10+rpi1),
libcom-err2 (= 1.46.6~rc1-1),
libcrypt-dev (= 1:4.4.33-1),
libcrypt1 (= 1:4.4.33-1),
libctf-nobfd0 (= 2.39.50.20221208-5+rpi1),
libctf0 (= 2.39.50.20221208-5+rpi1),
libcurl4 (= 7.87.0-1),
libdb5.3 (= 5.3.28+dfsg1-0.10),
libdebconfclient0 (= 0.265),
libdebhelper-perl (= 13.11.4),
libdeflate-dev (= 1.14-1),
libdeflate0 (= 1.14-1),
libdpkg-perl (= 1.21.9+rpi1),
libdrm-amdgpu1 (= 2.4.114-1+rpi1),
libdrm-common (= 2.4.114-1+rpi1),
libdrm-nouveau2 (= 2.4.114-1+rpi1),
libdrm-radeon1 (= 2.4.114-1+rpi1),
libdrm2 (= 2.4.114-1+rpi1),
libedit2 (= 3.1-20221030-2),
libelf1 (= 0.187-2+rpi2),
libevent-2.1-7 (= 2.1.12-stable-5+b1),
libevent-core-2.1-7 (= 2.1.12-stable-5+b1),
libevent-dev (= 2.1.12-stable-5+b1),
libevent-extra-2.1-7 (= 2.1.12-stable-5+b1),
libevent-openssl-2.1-7 (= 2.1.12-stable-5+b1),
libevent-pthreads-2.1-7 (= 2.1.12-stable-5+b1),
libexpat1 (= 2.5.0-1),
libfabric1 (= 1.11.0-3),
libffi8 (= 3.4.4-1),
libfftw3-bin (= 3.3.10-1),
libfftw3-dev (= 3.3.10-1),
libfftw3-double3 (= 3.3.10-1),
libfftw3-single3 (= 3.3.10-1),
libfido2-1 (= 1.12.0-2),
libfile-stripnondeterminism-perl (= 1.13.0-2),
libfltk-cairo1.3 (= 1.3.8-5+b1),
libfltk-forms1.3 (= 1.3.8-5+b1),
libfltk-gl1.3 (= 1.3.8-5+b1),
libfltk-images1.3 (= 1.3.8-5+b1),
libfltk1.3 (= 1.3.8-5+b1),
libfltk1.3-dev (= 1.3.8-5+b1),
libfontconfig1 (= 2.13.1-4.5),
libfreetype6 (= 2.12.1+dfsg-3),
libgcc-12-dev (= 12.2.0-10+rpi1),
libgcc-s1 (= 12.2.0-10+rpi1),
libgcrypt20 (= 1.10.1-3),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgfortran-12-dev (= 12.2.0-10+rpi1),
libgfortran5 (= 12.2.0-10+rpi1),
libgl1 (= 1.5.0-1),
libgl1-mesa-dri (= 22.2.0-1+rpi1),
libglapi-mesa (= 22.2.0-1+rpi1),
libglvnd0 (= 1.5.0-1),
libglx-mesa0 (= 22.2.0-1+rpi1),
libglx0 (= 1.5.0-1),
libgmp10 (= 2:6.2.1+dfsg1-1.1),
libgnutls30 (= 3.7.8-4),
libgomp1 (= 12.2.0-10+rpi1),
libgpg-error0 (= 1.46-1),
libgssapi-krb5-2 (= 1.20.1-1),
libhogweed6 (= 3.8.1-2),
libhwloc-dev (= 2.9.0-1),
libhwloc-plugins (= 2.9.0-1),
libhwloc15 (= 2.9.0-1),
libibverbs-dev (= 42.0-1),
libibverbs1 (= 42.0-1),
libicu72 (= 72.1-3),
libidn2-0 (= 2.3.3-1),
libisl23 (= 0.25-1),
libjansson4 (= 2.14-2),
libjbig-dev (= 2.1-6.1),
libjbig0 (= 2.1-6.1),
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 (= 1.20.1-1),
libkeyutils1 (= 1.6.3-1),
libkrb5-3 (= 1.20.1-1),
libkrb5support0 (= 1.20.1-1),
libldap-2.5-0 (= 2.5.13+dfsg-2+rpi1+b1),
liblerc-dev (= 4.0.0+ds-2),
liblerc4 (= 4.0.0+ds-2),
libllvm14 (= 1:14.0.6-9+rpi1),
libltdl-dev (= 2.4.7-5),
libltdl7 (= 2.4.7-5),
liblz4-1 (= 1.9.4-1+rpi1),
liblzma-dev (= 5.4.0-0.1),
liblzma5 (= 5.4.0-0.1),
libmagic-mgc (= 1:5.41-4),
libmagic1 (= 1:5.41-4),
libmd0 (= 1.0.4-2),
libmount1 (= 2.38.1-4),
libmpc3 (= 1.2.1-2),
libmpfr6 (= 4.1.0-3),
libmunge2 (= 0.5.14-6),
libncursesw6 (= 6.3+20220423-2),
libnettle8 (= 3.8.1-2),
libnghttp2-14 (= 1.51.0-1),
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),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libnuma-dev (= 2.0.16-1),
libnuma1 (= 2.0.16-1),
libopenmpi-dev (= 4.1.4-3+rpi1),
libopenmpi3 (= 4.1.4-3+rpi1),
libp11-kit0 (= 0.24.1-1),
libpam-modules (= 1.5.2-5),
libpam-modules-bin (= 1.5.2-5),
libpam-runtime (= 1.5.2-5),
libpam0g (= 1.5.2-5),
libpciaccess0 (= 0.17-2),
libpcre2-8-0 (= 10.40-3),
libperl5.36 (= 5.36.0-6),
libpipeline1 (= 1.5.7-1),
libpixman-1-0 (= 0.42.2-1),
libpmix-dev (= 4.2.2-1),
libpmix2 (= 4.2.2-1),
libpng16-16 (= 1.6.39-2),
libproc2-0 (= 2:4.0.2-3),
libpsl5 (= 0.21.0-1.2),
libpthread-stubs0-dev (= 0.4-1),
librdmacm1 (= 42.0-1),
librhash0 (= 1.4.3-3),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg-10),
libsasl2-modules-db (= 2.1.28+dfsg-10),
libseccomp2 (= 2.5.4-1+rpi1),
libselinux1 (= 3.4-1),
libsemanage-common (= 3.4-1),
libsemanage2 (= 3.4-1),
libsensors-config (= 1:3.6.0-7.1),
libsensors5 (= 1:3.6.0-7.1),
libsepol2 (= 3.4-2),
libsmartcols1 (= 2.38.1-4),
libssh2-1 (= 1.10.0-3+b1),
libssl3 (= 3.0.7-1),
libstdc++-12-dev (= 12.2.0-10+rpi1),
libstdc++6 (= 12.2.0-10+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 252.2-1+rpi1),
libtasn1-6 (= 4.19.0-2),
libtiff-dev (= 4.5.0-3),
libtiff6 (= 4.5.0-3),
libtiffxx6 (= 4.5.0-3),
libtinfo6 (= 6.3+20220423-2),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-5),
libubsan1 (= 12.2.0-10+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 252.2-1+rpi1),
libunistring2 (= 1.0-2),
libuuid1 (= 2.38.1-4),
libuv1 (= 1.44.2-1+rpi1),
libwebp-dev (= 1.2.2-2+b1),
libwebp7 (= 1.2.2-2+b1),
libwebpdemux2 (= 1.2.2-2+b1),
libwebpmux3 (= 1.2.2-2+b1),
libx11-6 (= 2:1.8.3-3),
libx11-data (= 2:1.8.3-3),
libx11-dev (= 2:1.8.3-3),
libx11-xcb1 (= 2:1.8.3-3),
libxau-dev (= 1:1.0.9-1),
libxau6 (= 1:1.0.9-1),
libxcb-dri2-0 (= 1.15-1),
libxcb-dri3-0 (= 1.15-1),
libxcb-glx0 (= 1.15-1),
libxcb-present0 (= 1.15-1),
libxcb-render0 (= 1.15-1),
libxcb-shm0 (= 1.15-1),
libxcb-sync1 (= 1.15-1),
libxcb-xfixes0 (= 1.15-1),
libxcb1 (= 1.15-1),
libxcb1-dev (= 1.15-1),
libxcursor1 (= 1:1.2.1-1),
libxdmcp-dev (= 1:1.1.2-3),
libxdmcp6 (= 1:1.1.2-3),
libxext6 (= 2:1.3.4-1),
libxfixes3 (= 1:6.0.0-2),
libxft2 (= 2.3.6-1),
libxinerama1 (= 2:1.1.4-3),
libxml2 (= 2.9.14+dfsg-1.1),
libxnvctrl0 (= 510.108.03-1),
libxrender1 (= 1:0.9.10-1.1),
libxshmfence1 (= 1.3-1),
libxxf86vm1 (= 1:1.1.4-1+b2),
libz3-4 (= 4.8.12-3),
libzstd-dev (= 1.5.2+dfsg2-3),
libzstd1 (= 1.5.2+dfsg2-3),
linux-libc-dev (= 6.0.12-1+rpi1),
login (= 1:4.13+dfsg1-1),
m4 (= 1.4.19-2),
make (= 4.3-4.1),
man-db (= 2.11.1-1),
mawk (= 1.3.4.20200120-3.1),
ncurses-base (= 6.3+20220423-2),
ncurses-bin (= 6.3+20220423-2),
ocl-icd-libopencl1 (= 2.3.1-1),
openmpi-bin (= 4.1.4-3+rpi1),
openmpi-common (= 4.1.4-3+rpi1),
openssh-client (= 1:9.1p1-2),
passwd (= 1:4.13+dfsg1-1),
patch (= 2.7.6-7),
perl (= 5.36.0-6),
perl-base (= 5.36.0-6),
perl-modules-5.36 (= 5.36.0-6),
po-debconf (= 1.0.21+nmu1),
procps (= 2:4.0.2-3),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sgml-base (= 1.31),
sysvinit-utils (= 3.05-7),
tar (= 1.34+dfsg-1),
ucf (= 3.0043),
util-linux (= 2.38.1-4),
util-linux-extra (= 2.38.1-4),
x11proto-dev (= 2022.1-1),
xorg-sgml-doctools (= 1:1.11-1.1),
xtrans-dev (= 1.4.0-1),
xz-utils (= 5.4.0-0.1),
zlib1g (= 1:1.2.13.dfsg-1),
zlib1g-dev (= 1:1.2.13.dfsg-1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1673725088"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
relion-dbgsym_3.1.3-3+b1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 329863708 bytes: control archive=3084 bytes.
2599 bytes, 12 lines control
5916 bytes, 56 lines md5sums
Package: relion-dbgsym
Source: relion (3.1.3-3)
Version: 3.1.3-3+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 339130
Depends: relion (= 3.1.3-3+b1)
Section: debug
Priority: optional
Description: debug symbols for relion
Build-Ids: 0932ddb0b3c162463a3fdc36ccfbeab4cea51b3f 09587053fd1fb1ed0b9a8050ad4573955e7183a6 0ebdaa6c5b537811812b4d091bd165be71610e3c 15d98c242ca05bc2035d2f6a77d06d73011d0527 1745d252c781185950f0af52eef05c553e2171d6 1f50d9ca53001446b5b4b08ebf942e0c64649aa1 21a4ca991791bf4a4b5ac375f45662ba2eb4847f 21d8c7ca66a597656d2f24a3fde1cb25a331d6f8 227f40cc5fe7c4b01dabf80a677d8e31a0408a0d 24dde917461023b9b41c73b6fe2685417bca4654 257d5abb9c43c89410278e379972e8502e070cf8 28f1ddc15e21ff5a4f7a3d181de7ea2d674490db 2d31fe242d26a4494a21d4426bf75909a03a59a2 346afd0795b637c3d35d3cdb5a60a79068d5d4d3 363d6665603d360b664ac86b64839a86a6f94592 36c9aa4b80177d9202946d8fa89b31113845bd24 38635c6f0f4de0b1ad8a0cdbdd36546393c094a2 395fb29b76bc08996e2f0d48daf7a073a8b54889 39e8b6d1fb246c3d389c48044db7ee5cf9ab6716 40c0f6870dd5f1b033f9d31a9621af4777a70f42 4978cc6d230ef76a2c1e8d41538e678ad6683ec9 4d99ff516054dd2b3a9a7bfe1b1b597aae30b2de 51818c7782bf147f7d8fff7e487dcacd003f4082 525a507d576c54c358fc7704b845f24f38b840e5 52aca367223e90e696fcd465b5fb4e1be7cd4066 637ee54d0a4ea38090e23da59a2f037958446e3e 693352bf9c47f80ae5cdce0fdce65aed98bb5521 6b5293824ccc99a67757c749304a3c407804b916 6ce4b72d963f50544baca9b8d9532e707bf23012 6d4e51f60def77abaabcd5669bd0e253f4fa142c 6dd305ca998550bf16d523da013898839546111d 72a45face9ce492e6f434a9004a73f53f1d09174 775543a5b669272da0e6a64701f20b8fe9b79f5c 7abefa50e0f45c7f18f8dfccef0c1443b5ed9d5c 85e0912213b994308555d7344c67f42ae4eb0218 8daf8b20f7ee019d3a17441101f026bb3989fa43 9ae80a23c3ee5c6d2c9355099ed1dac287bbc963 a633de9016d00707fccf8452caebf949190176bf ad8f0ae9f88d6d5c6588002ba9a946db4ff60837 af19a7d8f2449bab56d58c0b2bfb234399b2bc57 b3d6a77c15b0183ee01d118a3a9a993113e0bc36 b45f5228d0aca7a64ac78ef63b178a601d6cbaaf bba42300aa9e0f70401dcdfbe676664b015d5ea9 c26527332b5d61cbb526f4dbeaf1aafe88de7bb1 c2cdc5c7c37b3f9af57e8b505bfd7aa00642be6a c2fd0a5a11febd944c1874964140cf92c51adc75 cc390eb94a1c6be4bebe3dcc558be6c372446a53 d328b32b2977c4d523644950defc8a459913c542 d63f750b6273cd9872e78cb214004c0c32b652c7 e488417b0ca3586775ac9b723cd4035457ed5ba6 f2fde77a2bb67bcb2245125c393a9ad9c1cc9f18 f9d23f1134304238dab6d23084a6c99c9b355a65 fb2572135509d2ca62f3ae00fe47d5f2437e52c7 fc26dabc9b397b3f1eb254190760954ad2670ff5 ff5cd61ae5d85f429036063244be592a0c902104
drwxr-xr-x root/root 0 2023-01-14 19:38 ./
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/lib/
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/lib/debug/.build-id/09/
-rw-r--r-- root/root 5465996 2023-01-14 19:38 ./usr/lib/debug/.build-id/09/32ddb0b3c162463a3fdc36ccfbeab4cea51b3f.debug
-rw-r--r-- root/root 3766816 2023-01-14 19:38 ./usr/lib/debug/.build-id/09/587053fd1fb1ed0b9a8050ad4573955e7183a6.debug
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root 4593948 2023-01-14 19:38 ./usr/lib/debug/.build-id/0e/bdaa6c5b537811812b4d091bd165be71610e3c.debug
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/lib/debug/.build-id/15/
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lrwxrwxrwx root/root 0 2023-01-14 19:38 ./usr/share/doc/relion-dbgsym -> relion
relion-gui-dbgsym_3.1.3-3+b1_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 19902676 bytes: control archive=704 bytes.
478 bytes, 12 lines control
408 bytes, 4 lines md5sums
Package: relion-gui-dbgsym
Source: relion (3.1.3-3)
Version: 3.1.3-3+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 20480
Depends: relion-gui (= 3.1.3-3+b1)
Section: debug
Priority: optional
Description: debug symbols for relion-gui
Build-Ids: 14b6cfeeab68192f05bbe1ccec832c804f294411 2dedaa3faeb3a80f6533a6a437f1e68eb70591a3 53e97c5dfbff51eea5142d48ac0c7bad76ed65dd
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lrwxrwxrwx root/root 0 2023-01-14 19:38 ./usr/share/doc/relion-gui-dbgsym -> relion-gui
relion-gui_3.1.3-3+b1_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 851776 bytes: control archive=1112 bytes.
1142 bytes, 22 lines control
472 bytes, 7 lines md5sums
Package: relion-gui
Source: relion (3.1.3-3)
Version: 3.1.3-3+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4319
Depends: relion (= 3.1.3-3+b1), libc6 (>= 2.34), libfftw3-double3 (>= 3.3.10), libfltk1.3 (>= 1.3.4), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libstdc++6 (>= 11), libtiff6 (>= 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.
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-rw-r--r-- root/root 15 2022-12-06 10:56 ./usr/share/lintian/overrides/relion-gui
relion_3.1.3-3+b1_armhf.deb
---------------------------
new Debian package, version 2.0.
size 9362604 bytes: control archive=2680 bytes.
1176 bytes, 23 lines control
4299 bytes, 67 lines md5sums
Package: relion
Source: relion (3.1.3-3)
Version: 3.1.3-3+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 75410
Depends: openmpi-gcc | openmpi-bin, libc6 (>= 2.34), libfftw3-double3 (>= 3.3.10), libfftw3-single3 (>= 3.3.10), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libopenmpi3 (>= 4.1.4), libstdc++6 (>= 11), libtiff6 (>= 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.
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-rwxr-xr-x root/root 1967880 2023-01-14 19:38 ./usr/bin/relion_flex_analyse
-rwxr-xr-x root/root 1967880 2023-01-14 19:38 ./usr/bin/relion_flex_analyse_mpi
-rwxr-xr-x root/root 984840 2023-01-14 19:38 ./usr/bin/relion_helix_inimodel2d
-rwxr-xr-x root/root 1312520 2023-01-14 19:38 ./usr/bin/relion_helix_toolbox
-rwxr-xr-x root/root 1050376 2023-01-14 19:38 ./usr/bin/relion_image_handler
-rwxr-xr-x root/root 919304 2023-01-14 19:38 ./usr/bin/relion_import
-rwxr-xr-x root/root 1640200 2023-01-14 19:38 ./usr/bin/relion_localsym
-rwxr-xr-x root/root 1705736 2023-01-14 19:38 ./usr/bin/relion_localsym_mpi
-rwxr-xr-x root/root 1312520 2023-01-14 19:38 ./usr/bin/relion_mask_create
-rwxr-xr-x root/root 853772 2023-01-14 19:38 ./usr/bin/relion_merge_particles
-rwxr-xr-x root/root 2361120 2023-01-14 19:38 ./usr/bin/relion_motion_refine
-rwxr-xr-x root/root 2361120 2023-01-14 19:38 ./usr/bin/relion_motion_refine_mpi
-rwxr-xr-x root/root 657160 2023-01-14 19:38 ./usr/bin/relion_mrc2vtk
-rwxr-xr-x root/root 1574668 2023-01-14 19:38 ./usr/bin/relion_particle_FCC
-rwxr-xr-x root/root 2492168 2023-01-14 19:38 ./usr/bin/relion_particle_reposition
-rwxr-xr-x root/root 1246988 2023-01-14 19:38 ./usr/bin/relion_particle_select
-rwxr-xr-x root/root 2492172 2023-01-14 19:38 ./usr/bin/relion_particle_subtract
-rwxr-xr-x root/root 2492168 2023-01-14 19:38 ./usr/bin/relion_particle_subtract_mpi
-rwxr-xr-x root/root 984844 2023-01-14 19:38 ./usr/bin/relion_particle_symmetry_expand
-rwxr-xr-x root/root 1246984 2023-01-14 19:38 ./usr/bin/relion_pipeliner
-rwxr-xr-x root/root 1246984 2023-01-14 19:38 ./usr/bin/relion_plot_delocalisation
-rwxr-xr-x root/root 788236 2023-01-14 19:38 ./usr/bin/relion_postprocess
-rwxr-xr-x root/root 788236 2023-01-14 19:38 ./usr/bin/relion_postprocess_mpi
-rwxr-xr-x root/root 722696 2023-01-14 19:38 ./usr/bin/relion_prepare_subtomo
-rwxr-xr-x root/root 1312524 2023-01-14 19:38 ./usr/bin/relion_preprocess
-rwxr-xr-x root/root 1378060 2023-01-14 19:38 ./usr/bin/relion_preprocess_mpi
-rwxr-xr-x root/root 1902344 2023-01-14 19:38 ./usr/bin/relion_project
-rwxr-xr-x root/root 1902348 2023-01-14 19:38 ./usr/bin/relion_reconstruct
-rwxr-xr-x root/root 1967884 2023-01-14 19:38 ./usr/bin/relion_reconstruct_mpi
-rwxr-xr-x root/root 2426632 2023-01-14 19:38 ./usr/bin/relion_refine
-rwxr-xr-x root/root 2557704 2023-01-14 19:38 ./usr/bin/relion_refine_mpi
-rwxr-xr-x root/root 1574664 2023-01-14 19:38 ./usr/bin/relion_reposition
-rwxr-xr-x root/root 984840 2023-01-14 19:38 ./usr/bin/relion_run_ctffind
-rwxr-xr-x root/root 984840 2023-01-14 19:38 ./usr/bin/relion_run_ctffind_mpi
-rwxr-xr-x root/root 1246984 2023-01-14 19:38 ./usr/bin/relion_run_motioncorr
-rwxr-xr-x root/root 1246984 2023-01-14 19:38 ./usr/bin/relion_run_motioncorr_mpi
-rwxr-xr-x root/root 1771272 2023-01-14 19:38 ./usr/bin/relion_scheduler
-rwxr-xr-x root/root 919304 2023-01-14 19:38 ./usr/bin/relion_stack_create
-rwxr-xr-x root/root 1055 2023-01-14 19:38 ./usr/bin/relion_star_datablock_ctfdat
-rwxr-xr-x root/root 714 2023-01-14 19:38 ./usr/bin/relion_star_datablock_singlefiles
-rwxr-xr-x root/root 767 2023-01-14 19:38 ./usr/bin/relion_star_datablock_stack
-rwxr-xr-x root/root 984840 2023-01-14 19:38 ./usr/bin/relion_star_handler
-rwxr-xr-x root/root 675 2023-01-14 19:38 ./usr/bin/relion_star_loopheader
-rwxr-xr-x root/root 1217 2023-01-14 19:38 ./usr/bin/relion_star_plottable
-rwxr-xr-x root/root 2263 2023-01-14 19:38 ./usr/bin/relion_star_printtable
-rwxr-xr-x root/root 591624 2023-01-14 19:38 ./usr/bin/relion_tiltpair_plot
-rwxr-xr-x root/root 1246984 2023-01-14 19:38 ./usr/bin/relion_tomo_test
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/share/
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-01-14 19:38 ./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 217 2023-01-14 19:38 ./usr/share/doc/relion/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1086 2023-01-14 19:38 ./usr/share/doc/relion/changelog.Debian.gz
-rw-r--r-- root/root 7408 2022-12-06 10:56 ./usr/share/doc/relion/copyright
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/share/lintian/
drwxr-xr-x root/root 0 2023-01-14 19:38 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 15 2022-12-06 10:56 ./usr/share/lintian/overrides/relion
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 4062556
Build-Time: 2314
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 973
Job: relion_3.1.3-3
Machine Architecture: armhf
Package: relion
Package-Time: 3322
Source-Version: 3.1.3-3
Space: 4062556
Status: successful
Version: 3.1.3-3+b1
--------------------------------------------------------------------------------
Finished at 2023-01-14T20:16:42Z
Build needed 00:55:22, 4062556k disk space