seer →
1.1.4-7 →
armhf → 2022-11-09 04:10:19
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| seer 1.1.4-7 (armhf) Wed, 09 Nov 2022 03:56:08 +0000 |
+==============================================================================+
Package: seer
Version: 1.1.4-7
Source Version: 1.1.4-7
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-511efd2f-3e77-4036-b89c-a16bdd0e9d47' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.2 MB]
Fetched 27.7 MB in 12s (2256 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'seer' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/seer.git
Please use:
git clone https://salsa.debian.org/med-team/seer.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 984 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main seer 1.1.4-7 (dsc) [2172 B]
Get:2 http://172.17.4.1/private bookworm-staging/main seer 1.1.4-7 (tar) [972 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main seer 1.1.4-7 (diff) [9180 B]
Fetched 984 kB in 0s (4972 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/seer-eGA0N8/seer-1.1.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-eGA0N8' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-jZKzRi/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-jZKzRi/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-jZKzRi/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (3543 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap libperl5.34 netbase perl-modules-5.34 sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 42 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (35.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14774 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libarmadillo-dev, libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev
Filtered Build-Depends: debhelper-compat (= 13), libarmadillo-dev, libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev
dpkg-deb: building package 'sbuild-build-depends-seer-dummy' in '/<<BUILDDIR>>/resolver-jZKzRi/apt_archive/sbuild-build-depends-seer-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-seer-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ Sources [536 B]
Get:5 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ Packages [616 B]
Fetched 2485 B in 1s (3840 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install seer 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 libperl5.34 netbase perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarmadillo-dev libarmadillo11 libarpack2
libarpack2-dev libblas-dev libblas3 libboost-dev
libboost-program-options-dev libboost-program-options1.74-dev
libboost-program-options1.74.0 libboost1.74-dev libbrotli1 libbsd0 libcurl4
libcurl4-openssl-dev libdebhelper-perl libdlib-data libdlib-dev libdlib19.1
libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2
libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5
libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgzstream-dev
libgzstream0 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhwloc15 libicu71
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3
libllvm14 libmagic-mgc libmagic1 libmd0 libnghttp2-14 libopencv-core-dev
libopencv-core406 libpipeline1 libpng-dev libpng16-16 libpsl5
libpthread-stubs0-dev librtmp1 libsensors-config libsensors5 libsqlite3-dev
libssh2-1 libssl-dev libssl3 libsub-override-perl libsuperlu-dev libsuperlu5
libsz2 libtbb-dev libtbb12 libtbbbind-2-5 libtbbmalloc2 libtool libuchardet0
libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1
libxcb-xfixes0 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6
libxfixes3 libxml2 libxshmfence1 libxxf86vm1 libz3-4 m4 man-db po-debconf
pybind11-dev x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libitpp-dev liblapack-doc
libboost-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
pkg-config libhdf5-doc lm-sensors sqlite3-doc libssl-doc libsuperlu-doc
libtbb-doc libtool-doc gfortran | fortran95-compiler gcj-jdk libx11-doc
libxcb-doc m4-doc apparmor less www-browser libmail-box-perl pybind11-doc
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libhwloc-plugins
libpng-tools publicsuffix libltdl-dev libmail-sendmail-perl libeigen3-dev
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarmadillo-dev libarmadillo11 libarpack2
libarpack2-dev libblas-dev libblas3 libboost-dev
libboost-program-options-dev libboost-program-options1.74-dev
libboost-program-options1.74.0 libboost1.74-dev libbrotli1 libbsd0 libcurl4
libcurl4-openssl-dev libdebhelper-perl libdlib-data libdlib-dev libdlib19.1
libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2
libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5
libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgzstream-dev
libgzstream0 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhwloc15 libicu71
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3
libllvm14 libmagic-mgc libmagic1 libmd0 libnghttp2-14 libopencv-core-dev
libopencv-core406 libpipeline1 libpng-dev libpng16-16 libpsl5
libpthread-stubs0-dev librtmp1 libsensors-config libsensors5 libsqlite3-dev
libssh2-1 libssl-dev libsub-override-perl libsuperlu-dev libsuperlu5 libsz2
libtbb-dev libtbb12 libtbbbind-2-5 libtbbmalloc2 libtool libuchardet0
libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1
libxcb-xfixes0 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6
libxfixes3 libxml2 libxshmfence1 libxxf86vm1 libz3-4 m4 man-db po-debconf
pybind11-dev sbuild-build-depends-seer-dummy x11proto-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
The following packages will be upgraded:
libssl3
1 upgraded, 128 newly installed, 0 to remove and 41 not upgraded.
Need to get 153 MB of archives.
After this operation, 575 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-jZKzRi/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1.1 [78.2 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.0-1 [1299 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10.1 [79.9 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10.1 [940 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf hdf5-helpers armhf 1.10.8+repack-1 [45.1 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libsz2 armhf 1.0.6-1 [7452 B]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libaec-dev armhf 1.0.6-1 [17.6 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-3+rpi1 [238 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libarpack2 armhf 3.8.0-1 [85.9 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libsuperlu5 armhf 5.3.0+dfsg1-2 [128 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libarmadillo11 armhf 1:11.4.2+dfsg-1 [96.4 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.1-2 [114 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.1-2 [2847 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libarpack2-dev armhf 3.8.0-1 [94.6 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.7-1 [1614 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.86.0-1 [321 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-103-1 armhf 1.10.8+repack-1 [1235 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-fortran-102 armhf 1.10.8+repack-1 [98.7 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-100 armhf 1.10.8+repack-1 [81.7 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.8+repack-1 [56.0 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.8+repack-1 [133 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.8+repack-1 [42.4 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-openssl-dev armhf 7.86.0-1 [398 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.7-1 [2095 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-dev armhf 1.10.8+repack-1 [2325 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libsuperlu-dev armhf 5.3.0+dfsg1-2 [22.1 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libarmadillo-dev armhf 1:11.4.2+dfsg-1 [403 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-17 [9534 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b4 [4824 B]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libboost-program-options1.74.0 armhf 1.74.0-17 [332 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libboost-program-options1.74-dev armhf 1.74.0-17 [370 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libboost-program-options-dev armhf 1.74.0.3+b4 [4616 B]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libdlib-data all 19.24+dfsg-1 [63.4 MB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.38-2 [273 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libdlib19.1 armhf 19.24+dfsg-1 [3670 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libglvnd0 armhf 1.5.0-1 [51.5 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libdrm-common all 2.4.113-2+rpi1 [15.8 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libdrm2 armhf 2.4.113-2+rpi1 [41.6 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libglapi-mesa armhf 22.2.0-1+rpi1 [84.6 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libx11-xcb1 armhf 2:1.8.1-2 [203 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libxcb-glx0 armhf 1.15-1 [121 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libxcb-present0 armhf 1.15-1 [105 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libxcb-sync1 armhf 1.15-1 [108 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libxcb-xfixes0 armhf 1.15-1 [109 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libxfixes3 armhf 1:6.0.0-2 [21.2 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libxshmfence1 armhf 1.3-1 [8636 B]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.1 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libdrm-amdgpu1 armhf 2.4.113-2+rpi1 [28.4 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libdrm-nouveau2 armhf 2.4.113-2+rpi1 [26.0 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libdrm-radeon1 armhf 2.4.113-2+rpi1 [29.7 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20221030-1 [76.1 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libz3-4 armhf 4.8.12-3 [5798 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libllvm14 armhf 1:14.0.6-2+rpi1 [19.5 MB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libsensors5 armhf 1:3.6.0-7.1 [31.6 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libgl1-mesa-dri armhf 22.2.0-1+rpi1 [5593 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libglx-mesa0 armhf 22.2.0-1+rpi1 [171 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libglx0 armhf 1.5.0-1 [32.4 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libtbbmalloc2 armhf 2021.7.0-1+rpi1 [39.5 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libhwloc15 armhf 2.8.0-1 [130 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libtbbbind-2-5 armhf 2021.7.0-1+rpi1 [12.3 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libtbb12 armhf 2021.7.0-1+rpi1 [65.6 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libopencv-core406 armhf 4.6.0+dfsg-7+rpi1 [808 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf libtbb-dev armhf 2021.7.0-1+rpi1 [191 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libopencv-core-dev armhf 4.6.0+dfsg-7+rpi1 [1634 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libpng-dev armhf 1.6.38-2 [352 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libsqlite3-dev armhf 3.39.4-1 [898 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf x11proto-dev all 2022.1-1 [599 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libxcb1-dev armhf 1.15-1 [175 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf libx11-dev armhf 2:1.8.1-2 [780 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf pybind11-dev all 2.10.0-2 [180 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf libdlib-dev armhf 19.24+dfsg-1 [2006 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf libgzstream0 armhf 1.5+git20171107.9a20658-1 [6504 B]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libgzstream-dev armhf 1.5+git20171107.9a20658-1 [6940 B]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up dh-autoreconf (20) ...
Setting up libxcb-sync1:armhf (1.15-1) ...
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Setting up libxcb-dri2-0:armhf (1.15-1) ...
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Setting up libllvm14:armhf (1:14.0.6-2+rpi1) ...
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Setting up dwz (0.14+20220924-2) ...
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Setting up libx11-6:armhf (2:1.8.1-2) ...
Setting up libsuperlu-dev:armhf (5.3.0+dfsg1-2) ...
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Setting up libxcb-dri3-0:armhf (1.15-1) ...
Setting up libx11-xcb1:armhf (2:1.8.1-2) ...
Setting up libdrm-nouveau2:armhf (2.4.113-2+rpi1) ...
Setting up libarpack2-dev:armhf (3.8.0-1) ...
Setting up libarmadillo11 (1:11.4.2+dfsg-1) ...
Setting up libdrm-radeon1:armhf (2.4.113-2+rpi1) ...
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 libtbb12:armhf (2021.7.0-1+rpi1) ...
Setting up man-db (2.11.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ...
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Setting up libcurl4-openssl-dev:armhf (7.86.0-1) ...
Setting up libhdf5-103-1:armhf (1.10.8+repack-1) ...
Setting up libhdf5-cpp-103-1:armhf (1.10.8+repack-1) ...
Setting up libtbb-dev:armhf (2021.7.0-1+rpi1) ...
Setting up libhdf5-hl-100:armhf (1.10.8+repack-1) ...
Setting up libglx-mesa0:armhf (22.2.0-1+rpi1) ...
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Setting up debhelper (13.10.1) ...
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Setting up libhdf5-fortran-102:armhf (1.10.8+repack-1) ...
Setting up libhdf5-hl-fortran-100:armhf (1.10.8+repack-1) ...
Setting up libopencv-core406:armhf (4.6.0+dfsg-7+rpi1) ...
Setting up libhdf5-dev (1.10.8+repack-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libopencv-core-dev:armhf (4.6.0+dfsg-7+rpi1) ...
Setting up libarmadillo-dev (1:11.4.2+dfsg-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up x11proto-dev (2022.1-1) ...
Setting up libxau-dev:armhf (1:1.0.9-1) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up libxcb1-dev:armhf (1.15-1) ...
Setting up libx11-dev:armhf (2:1.8.1-2) ...
Setting up libdlib-dev:armhf (19.24+dfsg-1) ...
Setting up sbuild-build-depends-seer-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-1.1 bsdutils_1:2.38.1-1.1 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hdf5-helpers_1.10.8+repack-1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libarmadillo-dev_1:11.4.2+dfsg-1 libarmadillo11_1:11.4.2+dfsg-1 libarpack2_3.8.0-1 libarpack2-dev_3.8.0-1 libasan8_12.2.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6+rpi1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38.1-1.1 libboost-dev_1.74.0.3+b4 libboost-program-options-dev_1.74.0.3+b4 libboost-program-options1.74-dev_1.74.0-17 libboost-program-options1.74.0_1.74.0-17 libboost1.74-dev_1.74.0-17 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-3+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libcurl4_7.86.0-1 libcurl4-openssl-dev_7.86.0-1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.10.1 libdlib-data_19.24+dfsg-1 libdlib-dev_19.24+dfsg-1 libdlib19.1_19.24+dfsg-1 libdpkg-perl_1.21.9+rpi1 libdrm-amdgpu1_2.4.113-2+rpi1 libdrm-common_2.4.113-2+rpi1 libdrm-nouveau2_2.4.113-2+rpi1 libdrm-radeon1_2.4.113-2+rpi1 libdrm2_2.4.113-2+rpi1 libedit2_3.1-20221030-1 libelf1_0.187-2+rpi2 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-3+rpi1 libgl1-mesa-dri_22.2.0-1+rpi1 libglapi-mesa_22.2.0-1+rpi1 libglvnd0_1.5.0-1 libglx-mesa0_22.2.0-1+rpi1 libglx0_1.5.0-1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-3+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.20-1 libgzstream-dev_1.5+git20171107.9a20658-1 libgzstream0_1.5+git20171107.9a20658-1 libhdf5-103-1_1.10.8+repack-1 libhdf5-cpp-103-1_1.10.8+repack-1 libhdf5-dev_1.10.8+repack-1 libhdf5-fortran-102_1.10.8+repack-1 libhdf5-hl-100_1.10.8+repack-1 libhdf5-hl-cpp-100_1.10.8+repack-1 libhdf5-hl-fortran-100_1.10.8+repack-1 libhogweed6_3.8.1-2 libhwloc15_2.8.0-1 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjpeg-dev_1:2.1.2-1 libjpeg62-turbo_1:2.1.2-1 libjpeg62-turbo-dev_1:2.1.2-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 libldap-2.5-0_2.5.13+dfsg-2+rpi1 libllvm14_1:14.0.6-2+rpi1 liblz4-1_1.9.4-1+rpi1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-1.1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopencv-core-dev_4.6.0+dfsg-7+rpi1 libopencv-core406_4.6.0+dfsg-7+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 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.6-3 libpng-dev_1.6.38-2 libpng16-16_1.6.38-2 libpsl5_0.21.0-1.2 libpthread-stubs0-dev_0.4-1 libreadline8_8.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsensors-config_1:3.6.0-7.1 libsensors5_1:3.6.0-7.1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1.1 libsqlite3-0_3.39.4-1 libsqlite3-dev_3.39.4-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.7-1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-4 libsuperlu-dev_5.3.0+dfsg1-2 libsuperlu5_5.3.0+dfsg1-2 libsystemd0_251.5-1+rpi1 libsz2_1.0.6-1 libtasn1-6_4.19.0-2 libtbb-dev_2021.7.0-1+rpi1 libtbb12_2021.7.0-1+rpi1 libtbbbind-2-5_2021.7.0-1+rpi1 libtbbmalloc2_2021.7.0-1+rpi1 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-1.1 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 libx11-dev_2:1.8.1-2 libx11-xcb1_2:1.8.1-2 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb-dri2-0_1.15-1 libxcb-dri3-0_1.15-1 libxcb-glx0_1.15-1 libxcb-present0_1.15-1 libxcb-shm0_1.15-1 libxcb-sync1_1.15-1 libxcb-xfixes0_1.15-1 libxcb1_1.15-1 libxcb1-dev_1.15-1 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 libxml2_2.9.14+dfsg-1 libxshmfence1_1.3-1 libxxf86vm1_1:1.1.4-1+b2 libxxhash0_0.8.1-1 libz3-4_4.8.12-3 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.0-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-1.1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 pybind11-dev_2.10.0-2 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seer-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 util-linux_2.38.1-1.1 util-linux-extra_2.38.1-1.1 x11proto-dev_2022.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.wap63Txk/trustedkeys.kbx': General error
gpgv: Signature made Sun Nov 6 14:42:46 2022 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./seer_1.1.4-7.dsc
dpkg-source: info: extracting seer in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking seer_1.1.4.orig.tar.gz
dpkg-source: info: unpacking seer_1.1.4-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_lib_location.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying gcc11.patch
dpkg-source: info: applying typos.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-511efd2f-3e77-4036-b89c-a16bdd0e9d47
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package seer
dpkg-buildpackage: info: source version 1.1.4-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -f *.o ~* seer kmds map_back combineKmers filter_seer
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
cd test && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
rm -f *.o ~* tests_passed
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- LDFLAGS+=-L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make -j4 "INSTALL=install --strip-program=true" LDFLAGS\+=-L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o sample.o sample.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o significant_kmer.o significant_kmer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmer.o kmer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o covar.o covar.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCommon.o seerCommon.cpp
In file included from /usr/include/armadillo:22,
from kmer.hpp:9,
from kmer.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerErr.o seerErr.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerIO.o seerIO.cpp
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from seerCommon.cpp:9:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from seerErr.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerBasicFilter.o seerBasicFilter.cpp
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from seerIO.cpp:12:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
seerCommon.cpp: In function 'arma::vec dlib_to_arma(const column_vector&)':
seerCommon.cpp:174:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'long int' [-Wsign-compare]
174 | for (unsigned int i = 0; i < dlib_vec.nr(); ++i)
| ~~^~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from seerBasicFilter.cpp:10:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerMain.o seerMain.cpp
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from seercommon.hpp:15:
/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<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Distance = int; _Tp = arma::arma_sort_index_packet<double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_descend<double> >]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Distance = int; _Tp = arma::arma_sort_index_packet<double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_ascend<double> >]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<double> > > >' 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<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_descend<double> >]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<double> > > >' 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<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_ascend<double> >]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<double> > > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_ascend<double> >]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_descend<double> >]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<double> > > >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_descend<double> >]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Compare = arma::arma_sort_index_helper_descend<double>]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'bool arma::arma_sort_index_helper(Mat<unsigned int>&, const Proxy<T1>&, uword) [with T1 = Col<double>; bool sort_stable = false]' at /usr/include/armadillo_bits/op_sort_index_meat.hpp:96:16,
inlined from 'static bool arma::op_sort_index::apply_noalias(arma::Mat<unsigned int>&, const arma::Proxy<T1>&, arma::uword) [with T1 = arma::Col<double>]' at /usr/include/armadillo_bits/op_sort_index_meat.hpp:123:42,
inlined from 'static void arma::op_sort_index::apply(arma::Mat<unsigned int>&, const arma::mtOp<unsigned int, T1, arma::op_sort_index>&) [with T1 = arma::Col<double>]' at /usr/include/armadillo_bits/op_sort_index_meat.hpp:153:47,
inlined from 'arma::Mat<eT>& arma::Mat<eT>::operator=(const arma::mtOp<eT, T1, op_type>&) [with T1 = arma::Col<double>; op_type = arma::op_sort_index; eT = unsigned int]' at /usr/include/armadillo_bits/Mat_meat.hpp:5228:17,
inlined from 'arma::Col<eT>::Col(const arma::Base<eT, T1>&) [with T1 = arma::mtOp<unsigned int, arma::Col<double>, arma::op_sort_index>; eT = unsigned int]' at /usr/include/armadillo_bits/Col_meat.hpp:464:21,
inlined from 'static bool arma::op_pinv::apply_sym(arma::Mat<eT>&, const arma::Mat<eT>&, typename arma::get_pod_type<eT>::result, arma::uword) [with eT = double]' at /usr/include/armadillo_bits/op_pinv_meat.hpp:227:14:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_descend<double> >]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<arma::arma_sort_index_helper_descend<double> >]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, vector<arma::arma_sort_index_packet<double>, allocator<arma::arma_sort_index_packet<double> > > >; _Compare = arma::arma_sort_index_helper_descend<double>]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'bool arma::arma_sort_index_helper(Mat<unsigned int>&, const Proxy<T1>&, uword) [with T1 = Col<double>; bool sort_stable = false]' at /usr/include/armadillo_bits/op_sort_index_meat.hpp:96:16,
inlined from 'static bool arma::op_sort_index::apply_noalias(arma::Mat<unsigned int>&, const arma::Proxy<T1>&, arma::uword) [with T1 = arma::Col<double>]' at /usr/include/armadillo_bits/op_sort_index_meat.hpp:123:42,
inlined from 'static void arma::op_sort_index::apply(arma::Mat<unsigned int>&, const arma::mtOp<unsigned int, T1, arma::op_sort_index>&) [with T1 = arma::Col<double>]' at /usr/include/armadillo_bits/op_sort_index_meat.hpp:153:47,
inlined from 'arma::Mat<eT>& arma::Mat<eT>::operator=(const arma::mtOp<eT, T1, op_type>&) [with T1 = arma::Col<double>; op_type = arma::op_sort_index; eT = unsigned int]' at /usr/include/armadillo_bits/Mat_meat.hpp:5228:17,
inlined from 'arma::Col<eT>::Col(const arma::Base<eT, T1>&) [with T1 = arma::mtOp<unsigned int, arma::Col<double>, arma::op_sort_index>; eT = unsigned int]' at /usr/include/armadillo_bits/Col_meat.hpp:464:21,
inlined from 'static bool arma::op_pinv::apply_sym(arma::Mat<eT>&, const arma::Mat<eT>&, typename arma::get_pod_type<eT>::result, arma::uword) [with eT = double]' at /usr/include/armadillo_bits/op_pinv_meat.hpp:227:14:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<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<arma::arma_sort_index_packet<double>*, std::vector<arma::arma_sort_index_packet<double>, std::allocator<arma::arma_sort_index_packet<double> > > >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCmdLine.o seerCmdLine.cpp
In file included from /usr/include/c++/12/bits/stl_algobase.h:71,
from /usr/include/c++/12/string:50,
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 seercommon.hpp:10:
/usr/include/c++/12/bits/predefined_ops.h: In function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Iterator2 = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Compare = bool (*)(Sample, Sample)]':
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerStats.o seerStats.cpp
In file included from /usr/include/c++/12/vector:70,
from seercommon.hpp:18:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Sample&}; _Tp = Sample; _Alloc = std::allocator<Sample>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Sample>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from seercommon.hpp:15:
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' 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<Sample*, std::vector<Sample> >' 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 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, std::allocator<long long int> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerCmdLine.cpp:9:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
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 'static bool arma::diskio::save_hdf5_binary(const arma::Mat<eT>&, const arma::hdf5_name&, std::string&) [with eT = double]' at /usr/include/armadillo_bits/diskio_meat.hpp:1230:25:
/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, std::allocator<long long int> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerStats.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
In file included from /usr/include/c++/12/bits/stl_algo.h:60:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Distance = int; _Tp = Sample; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(Sample, Sample)>]':
/usr/include/c++/12/bits/stl_heap.h:135:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
135 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/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<Sample*, vector<Sample> >; _Distance = int; _Tp = Sample; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' 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<Sample*, vector<Sample> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' 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<Sample*, std::vector<Sample> >' changed in GCC 7.1
In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]',
inlined from '_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]' at /usr/include/c++/12/bits/stl_algo.h:1887:34,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]' at /usr/include/c++/12/bits/stl_algo.h:1921:38:
/usr/include/c++/12/bits/stl_algo.h:85:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
85 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:87:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
87 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:89:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
89 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:94:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
94 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:96:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
96 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]',
inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]' at /usr/include/c++/12/bits/stl_algo.h:1900:25,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]' at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1629 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Sample; _Alloc = std::allocator<Sample>]',
inlined from 'void readPheno(const std::string&, std::vector<Sample>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&)' at seerIO.cpp:36:24:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' 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<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = bool (*)(Sample, Sample)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void readPheno(const std::string&, std::vector<Sample>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&)' at seerIO.cpp:41:13:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' 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<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Sample*, vector<Sample> >; _Compare = bool (*)(Sample, Sample)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void readPheno(const std::string&, std::vector<Sample>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&)' at seerIO.cpp:41:13:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' 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<Sample*, std::vector<Sample> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from seercommon.hpp:18:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Kmer&}; _Tp = Kmer; _Alloc = std::allocator<Kmer>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Kmer>::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 = Kmer; _Alloc = std::allocator<Kmer>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Kmer; _Alloc = std::allocator<Kmer>]',
inlined from 'int main(int, char**)' at seerMain.cpp:158:36:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerContinuousAssoc.o seerContinuousAssoc.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerBinaryAssoc.o seerBinaryAssoc.cpp
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o logitFunction.o logitFunction.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o linearFunction.o linearFunction.cpp
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from logitFunction.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from linearFunction.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
In file included from /usr/include/c++/12/vector:70,
from seercommon.hpp:18:
/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:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Significant_kmer::add_covar_p(double)' at significant_kmer.hpp:52:70,
inlined from 'void doLinear(Kmer&, const arma::vec&, const arma::mat&)' at seerContinuousAssoc.cpp:113:20:
/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsMain.o kmdsMain.cpp
In file included from /usr/include/c++/12/vector:70,
from seercommon.hpp:18:
/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>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsStruct.o kmdsStruct.cpp
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const arma::Col<double>&}; _Tp = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<arma::Col<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 = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]',
inlined from 'void newtonRaphson(Kmer&, const arma::vec&, const arma::mat&, bool)' at seerBinaryAssoc.cpp:144:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<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 = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]',
inlined from 'void newtonRaphson(Kmer&, const arma::vec&, const arma::mat&, bool)' at seerBinaryAssoc.cpp:185:37:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsCmdLine.o kmdsCmdLine.cpp
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Significant_kmer::add_covar_p(double)' at significant_kmer.hpp:52:70,
inlined from 'void newtonRaphson(Kmer&, const arma::vec&, const arma::mat&, bool)' at seerBinaryAssoc.cpp:255:23:
/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 Significant_kmer::add_covar_p(double)' at significant_kmer.hpp:52:70,
inlined from 'void doLogit(Kmer&, const arma::vec&, const arma::mat&)' at seerBinaryAssoc.cpp:100:29:
/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 file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from kmds.hpp:9,
from kmdsMain.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o fasta.o fasta.cpp
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
In file included from /usr/include/armadillo:22,
from seercommon.hpp:35,
from kmds.hpp:9,
from kmdsCmdLine.cpp:8:
/usr/include/armadillo_bits/config.hpp:338:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/usr/include/armadillo_bits/config.hpp:343:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/usr/include/armadillo_bits/config.hpp:346:61: note: '#pragma message: INFO: see the documentation for details'
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapMain.o mapMain.cpp
In file included from /usr/include/c++/12/vector:70,
from seercommon.hpp:18:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const DistanceElement&}; _Tp = DistanceElement; _Alloc = std::allocator<DistanceElement>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<DistanceElement>::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 = DistanceElement; _Alloc = std::allocator<DistanceElement>]',
inlined from 'arma::mat dissimiliarityMatrix(const arma::mat&, unsigned int)' at kmdsStruct.cpp:114:35:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DistanceElement*, std::vector<DistanceElement> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from seercommon.hpp:18:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {arma::Col<double>}; _Tp = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<arma::Col<double> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapCmdLine.o mapCmdLine.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineInit.o combineInit.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineCmdLine.o combineCmdLine.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineKmers.o combineKmers.cpp
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {arma::Col<double>}; _Tp = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'int main(int, char**)' at kmdsMain.cpp:169:38:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filter_seer.o filter_seer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filterCmdLine.o filterCmdLine.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o seerMain.o seerCmdLine.o seerStats.o seerContinuousAssoc.o seerBinaryAssoc.o logitFunction.o linearFunction.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o seer
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o kmdsMain.o kmdsStruct.o kmdsCmdLine.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o kmds
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial fasta.o significant_kmer.o mapMain.o mapCmdLine.o -lboost_program_options -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o map_back
In file included from /usr/include/c++/12/list:63,
from filter_seer.hpp:11,
from filter_seer.cpp:7:
/usr/include/c++/12/bits/stl_list.h: In member function 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const Significant_kmer&}; _Tp = Significant_kmer; _Alloc = std::allocator<Significant_kmer>]':
/usr/include/c++/12/bits/stl_list.h:2003:8: note: parameter passing for argument of type 'std::__cxx11::list<Significant_kmer>::iterator' changed in GCC 7.1
2003 | _M_insert(iterator __position, _Args&&... __args)
| ^~~~~~~~~
In member function 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Significant_kmer; _Alloc = std::allocator<Significant_kmer>]',
inlined from 'int main(int, char**)' at filter_seer.cpp:96:43:
/usr/include/c++/12/bits/stl_list.h:1306:24: note: parameter passing for argument of type 'std::_List_iterator<Significant_kmer>' changed in GCC 7.1
1306 | { this->_M_insert(end(), __x); }
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial combineInit.o combineCmdLine.o combineKmers.o -lgzstream -lz -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o combineKmers
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial significant_kmer.o filter_seer.o filterCmdLine.o -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o filter_seer
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if dh_auto_test ; then echo Test passed ; else echo '****************************** TEST FAILED. Please contact upstream *******************************' ; fi
make -j4 test
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
cd test && make test
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
./run_test.pl && touch tests_passed
PASSED test 1, basic filters
PASSED test 2, binary phenotype assocation
PASSED test 3, print output
PASSED test 4, continuous phenotype assocation
PASSED test 5, assocation with population structure
PASSED test 6, assocation with covariates
PASSED test 7, filter output
PASSED test 8, map k-mers
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
Test passed
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>>'
dh_auto_install -- PREFIX=/<<PKGBUILDDIR>>/debian/seer/usr
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/seer AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/<<PKGBUILDDIR>>/debian/seer/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
cd src && make install
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
install -d /<<PKGBUILDDIR>>/debian/seer/usr/bin
install seer kmds map_back combineKmers filter_seer /<<PKGBUILDDIR>>/debian/seer/usr/bin
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
for pl in scripts/*.pl ; do \
plbase=`basename ${pl} .pl` ; \
sed "s+Usage: ./${plbase}.pl+Usage: ${plbase}+" ${pl} > /<<PKGBUILDDIR>>/debian/seer/usr/bin/${plbase} ; \
done
# Fix broken usage hint:
sed -i "s+Usage: ./hits_to_matrix.pl+Usage: reformat_output+" /<<PKGBUILDDIR>>/debian/seer/usr/bin/reformat_output
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian -name Makefile -exec chmod -x \{\} \;
find debian -name "*.fa" -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/seer/usr/bin/kmds contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/seer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/map_back contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/filter_seer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/combineKmers 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/seer/usr/bin/kmds debian/seer/usr/bin/seer debian/seer/usr/bin/map_back debian/seer/usr/bin/filter_seer debian/seer/usr/bin/combineKmers were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/combineKmers was not linked against libz.so.1 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'seer-dbgsym' in '../seer-dbgsym_1.1.4-7_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.4-7_armhf.deb'.
dpkg-genbuildinfo --build=any -O../seer_1.1.4-7_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../seer_1.1.4-7_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-11-09T04:10:13Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.4-7_armhf.changes:
---------------------------
Format: 1.8
Date: Sun, 06 Nov 2022 15:38:02 +0100
Source: seer
Binary: seer seer-dbgsym
Architecture: armhf
Version: 1.1.4-7
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
seer - genomic sequence element (kmer) enrichment analysis
Changes:
seer (1.1.4-7) unstable; urgency=medium
.
* d/watch: repair github changes; move to git mode.
* Standards-Version: 4.6.1 (routine-update)
* typos.patch: add; fix typos caught by lintian.
* d/m/blastn_to_phandango.1: new manual page.
* d/control: add myself to uploaders.
* d/copyright: refresh debian/ copyright years.
Checksums-Sha1:
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6b902cc6071107ff408e0542d9bb49e116419121 8244 seer_1.1.4-7_armhf.buildinfo
9a28923e86ff709d7489f083fdacc5ba65b898c7 1068148 seer_1.1.4-7_armhf.deb
Checksums-Sha256:
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1bc0aab8c584664c17048c6b8d61a940294be1c1974c0b80f35edd1d1efbc398 8244 seer_1.1.4-7_armhf.buildinfo
5f99efe4a53eeb442ab4c2167f56e5fb8523d7c6fd1374e71710d08f89c39ef0 1068148 seer_1.1.4-7_armhf.deb
Files:
075e8400d12c99edafd99f3a30adac27 8719624 debug optional seer-dbgsym_1.1.4-7_armhf.deb
452ce7dc730e6433290300479919cd52 8244 science optional seer_1.1.4-7_armhf.buildinfo
2af729fc7970b02d6c46b6b8932223d1 1068148 science optional seer_1.1.4-7_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.4-7_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 8719624 bytes: control archive=800 bytes.
523 bytes, 12 lines control
614 bytes, 6 lines md5sums
Package: seer-dbgsym
Source: seer
Version: 1.1.4-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8978
Depends: seer (= 1.1.4-7)
Section: debug
Priority: optional
Description: debug symbols for seer
Build-Ids: 2c30224f2319bf227286caf5c81576d58ac466bf 47cd7f6004207ef90004744ada6336259cc3e0e6 606b07ba3dde89b23156cc1657958059fe1a3a26 77593d6f2995dc4cf05d74b2d823f93dba2a2869 bf95d4f4cd51f59867f7eb8af43cc5e225f7a999
drwxr-xr-x root/root 0 2022-11-06 14:38 ./
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/2c/
-rw-r--r-- root/root 2754252 2022-11-06 14:38 ./usr/lib/debug/.build-id/2c/30224f2319bf227286caf5c81576d58ac466bf.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/47/
-rw-r--r-- root/root 3464736 2022-11-06 14:38 ./usr/lib/debug/.build-id/47/cd7f6004207ef90004744ada6336259cc3e0e6.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/60/
-rw-r--r-- root/root 392680 2022-11-06 14:38 ./usr/lib/debug/.build-id/60/6b07ba3dde89b23156cc1657958059fe1a3a26.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/77/
-rw-r--r-- root/root 922840 2022-11-06 14:38 ./usr/lib/debug/.build-id/77/593d6f2995dc4cf05d74b2d823f93dba2a2869.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 481400 2022-11-06 14:38 ./usr/lib/debug/.build-id/bf/95d4f4cd51f59867f7eb8af43cc5e225f7a999.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 1157880 2022-11-06 14:38 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/seer.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/share/
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-11-06 14:38 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.4-7_armhf.deb
----------------------
new Debian package, version 2.0.
size 1068148 bytes: control archive=2684 bytes.
1433 bytes, 24 lines control
4326 bytes, 62 lines md5sums
Package: seer
Version: 1.1.4-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4574
Depends: libarmadillo11 (>= 1:11.4.2+dfsg), libblas3 | libblas.so.3, libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgzstream0 (>= 1.5+dfsg), libhdf5-103-1, libstdc++6 (>= 11), zlib1g (>= 1:1.1.4), libtext-csv-perl
Suggests: fsm-lite
Section: science
Priority: optional
Homepage: https://github.com/johnlees/seer
Description: genomic sequence element (kmer) enrichment analysis
Bacterial genomes vary extensively in terms of both gene content and
gene sequence - this plasticity hampers the use of traditional SNP-based
methods for identifying all genetic associations with phenotypic
variation. SEER provides a computationally scalable and widely
applicable statistical method for the identification of sequence
elements that are significantly enriched in a phenotype of interest.
SEER is applicable to even tens of thousands of genomes by counting variable-
length k-mers using a distributed string-mining algorithm. Robust
options are provided for association analysis that also correct for the
clonal population structure of bacteria. Using large collections of
genomes of the major human pathogen Streptococcus pneumoniae, SEER
identifies relevant previously characterised resistance determinants for
several antibiotics.
drwxr-xr-x root/root 0 2022-11-06 14:38 ./
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/bin/
-rwxr-xr-x root/root 4597 2022-11-06 14:38 ./usr/bin/R_mds
-rwxr-xr-x root/root 3794 2022-11-06 14:38 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 2152 2022-11-06 14:38 ./usr/bin/blastn_to_phandango
-rwxr-xr-x root/root 132748 2022-11-06 14:38 ./usr/bin/combineKmers
-rwxr-xr-x root/root 67212 2022-11-06 14:38 ./usr/bin/filter_seer
-rwxr-xr-x root/root 1869 2022-11-06 14:38 ./usr/bin/hits_to_fastq
-rwxr-xr-x root/root 460944 2022-11-06 14:38 ./usr/bin/kmds
-rwxr-xr-x root/root 198284 2022-11-06 14:38 ./usr/bin/map_back
-rwxr-xr-x root/root 3200 2022-11-06 14:38 ./usr/bin/mapping_to_phandango
-rwxr-xr-x root/root 1208 2022-11-06 14:38 ./usr/bin/mash2matrix
-rwxr-xr-x root/root 2295 2022-11-06 14:38 ./usr/bin/reformat_output
-rwxr-xr-x root/root 592048 2022-11-06 14:38 ./usr/bin/seer
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/share/
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/share/doc/seer/
-rw-r--r-- root/root 684 2022-11-06 14:38 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 328 2022-11-06 14:38 ./usr/share/doc/seer/README.source
-rw-r--r-- root/root 278 2022-11-06 14:38 ./usr/share/doc/seer/README.test
-rw-r--r-- root/root 870 2022-11-06 14:38 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1176 2022-11-06 14:38 ./usr/share/doc/seer/copyright
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/share/doc/seer/examples/
-rw-r--r-- root/root 2168438 2017-06-20 09:43 ./usr/share/doc/seer/examples/6259_5_16.fa
-rw-r--r-- root/root 121 2017-06-20 09:43 ./usr/share/doc/seer/examples/Makefile
-rw-r--r-- root/root 196442 2017-06-20 09:43 ./usr/share/doc/seer/examples/all_structure_new
-rw-r--r-- root/root 29617 2017-06-20 09:43 ./usr/share/doc/seer/examples/all_structure_new.samples
-rw-r--r-- root/root 23 2017-06-20 09:43 ./usr/share/doc/seer/examples/assembly_locations.txt
-rw-r--r-- root/root 3011 2017-06-20 09:43 ./usr/share/doc/seer/examples/covariates.txt
-rw-r--r-- root/root 65372 2017-06-20 09:43 ./usr/share/doc/seer/examples/example.pheno
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 100472
Build-Time: 413
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 407
Job: seer_1.1.4-7
Machine Architecture: armhf
Package: seer
Package-Time: 845
Source-Version: 1.1.4-7
Space: 100472
Status: successful
Version: 1.1.4-7
--------------------------------------------------------------------------------
Finished at 2022-11-09T04:10:13Z
Build needed 00:14:05, 100472k disk space