seer →
1.1.4-7+b1 →
armhf → 2023-09-27 02:40:10
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| seer 1.1.4-7+b1 (armhf) Wed, 27 Sep 2023 02:25:05 +0000 |
+==============================================================================+
Package: seer
Version: 1.1.4-7+b1
Source Version: 1.1.4-7
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-3c0438d5-c1ab-4a8e-b3fa-db87ee74ffc9' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.1 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.6 MB]
Fetched 28.8 MB in 12s (2305 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/trixie-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 trixie-staging/main seer 1.1.4-7 (dsc) [2172 B]
Get:2 http://172.17.4.1/private trixie-staging/main seer 1.1.4-7 (tar) [972 kB]
Get:3 http://172.17.4.1/private trixie-staging/main seer 1.1.4-7 (diff) [9180 B]
Fetched 984 kB in 0s (5615 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/seer-gJGgYv/seer-1.1.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-gJGgYv' 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-Y3rj6l/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-Y3rj6l/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Y3rj6l/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-Y3rj6l/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Y3rj6l/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Y3rj6l/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Y3rj6l/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Y3rj6l/apt_archive ./ Packages [429 B]
Fetched 2105 B in 1s (2986 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils sgml-base util-linux-extra
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 16 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-Y3rj6l/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 (61.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11775 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-Y3rj6l/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-Y3rj6l/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Y3rj6l/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Y3rj6l/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Y3rj6l/apt_archive ./ Sources [536 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Y3rj6l/apt_archive ./ Packages [613 B]
Fetched 2482 B in 1s (4881 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 netbase sgml-base util-linux-extra
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 libarmadillo12 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 libicu72
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3
libllvm15 libmagic-mgc libmagic1 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 libsuperlu6
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-randr0 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 libidn-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 libpython3-dev
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 libarmadillo12 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 libicu72
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3
libllvm15 libmagic-mgc libmagic1 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 libsuperlu6 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-randr0 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 15 not upgraded.
Need to get 155 MB of archives.
After this operation, 585 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Y3rj6l/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libssl3 armhf 3.0.11-1 [1620 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-2 [1033 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-1 [80.5 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-3 [1342 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-13 [156 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.6 [81.9 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-13 [1201 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.6 [952 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf hdf5-helpers armhf 1.10.10+repack-2 [23.2 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libsz2 armhf 1.0.6-1 [7452 B]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libaec-dev armhf 1.0.6-1 [17.6 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 12.2.0-14+rpi1 [238 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libarpack2 armhf 3.8.0-3 [79.6 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libsuperlu6 armhf 6.0.1+dfsg1-1 [130 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libarmadillo12 armhf 1:12.6.1+dfsg-2 [98.7 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libblas-dev armhf 3.11.0-2 [106 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf liblapack-dev armhf 3.11.0-2 [3007 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libarpack2-dev armhf 3.8.0-3 [89.0 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.56.0-1 [60.5 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 7.88.1-10+rpi1 [343 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libhdf5-103-1 armhf 1.10.10+repack-2 [1213 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libhdf5-fortran-102 armhf 1.10.10+repack-2 [77.2 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libhdf5-hl-100 armhf 1.10.10+repack-2 [59.8 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.10+repack-2 [34.0 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.10+repack-2 [111 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.10+repack-2 [20.5 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2 [258 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libjpeg-dev armhf 1:2.1.5-2 [71.8 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libcurl4-openssl-dev armhf 7.88.1-10+rpi1 [423 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libssl-dev armhf 3.0.11-1 [2105 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libhdf5-dev armhf 1.10.10+repack-2 [2313 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libsuperlu-dev armhf 6.0.1+dfsg1-1 [21.5 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libarmadillo-dev armhf 1:12.6.1+dfsg-2 [408 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libboost1.74-dev armhf 1.74.0+ds1-22 [9511 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libboost-dev armhf 1.74.0.3+b4 [4824 B]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libboost-program-options1.74.0 armhf 1.74.0+ds1-22 [307 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libboost-program-options1.74-dev armhf 1.74.0+ds1-22 [345 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libboost-program-options-dev armhf 1.74.0.3+b4 [4616 B]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.7-4 [111 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libdlib-data all 19.24+dfsg-1 [63.4 MB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libpng16-16 armhf 1.6.40-1 [258 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libdlib19.1 armhf 19.24+dfsg-1 [3670 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libglvnd0 armhf 1.6.0-1 [53.8 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libx11-data all 2:1.8.6-1 [323 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.6-1 [726 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libdrm-common all 2.4.115-1+rpi1 [7324 B]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libdrm2 armhf 2.4.115-1+rpi1 [33.2 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libglapi-mesa armhf 23.1.7-1+rpi1 [46.1 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libx11-xcb1 armhf 2:1.8.6-1 [227 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libxcb-glx0 armhf 1.15-1 [121 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libxcb-present0 armhf 1.15-1 [105 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libxcb-randr0 armhf 1.15-1 [116 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libxcb-sync1 armhf 1.15-1 [108 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libxcb-xfixes0 armhf 1.15-1 [109 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libxfixes3 armhf 1:6.0.0-2 [21.2 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf libxshmfence1 armhf 1.3-1 [8636 B]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.1 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libdrm-amdgpu1 armhf 2.4.115-1+rpi1 [19.2 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libdrm-nouveau2 armhf 2.4.115-1+rpi1 [16.9 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libdrm-radeon1 armhf 2.4.115-1+rpi1 [20.6 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libedit2 armhf 3.1-20230828-1 [76.0 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libz3-4 armhf 4.8.12-3.1 [5797 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf libllvm15 armhf 1:15.0.6-4+rpi1+b1 [20.7 MB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libsensors-config all 1:3.6.0-8 [14.4 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf libsensors5 armhf 1:3.6.0-8 [31.7 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf libgl1-mesa-dri armhf 23.1.7-1+rpi1 [5778 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libglx-mesa0 armhf 23.1.7-1+rpi1 [130 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf libglx0 armhf 1.6.0-1 [32.0 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf libtbbmalloc2 armhf 2021.8.0-2+rpi1 [39.5 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libhwloc15 armhf 2.9.3-1 [124 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libtbbbind-2-5 armhf 2021.8.0-2+rpi1 [12.3 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf libtbb12 armhf 2021.8.0-2+rpi1 [65.7 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf libopencv-core406 armhf 4.6.0+dfsg-12+rpi1 [793 kB]
Get:114 http://172.17.4.1/private trixie-staging/main armhf libtbb-dev armhf 2021.8.0-2+rpi1 [192 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf libopencv-core-dev armhf 4.6.0+dfsg-12+rpi1 [1620 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf libpng-dev armhf 1.6.40-1 [336 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf libsqlite3-dev armhf 3.43.1-1 [925 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf x11proto-dev all 2023.2-1 [598 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:121 http://172.17.4.1/private trixie-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:122 http://172.17.4.1/private trixie-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:123 http://172.17.4.1/private trixie-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:124 http://172.17.4.1/private trixie-staging/main armhf libxcb1-dev armhf 1.15-1 [175 kB]
Get:125 http://172.17.4.1/private trixie-staging/main armhf libx11-dev armhf 2:1.8.6-1 [801 kB]
Get:126 http://172.17.4.1/private trixie-staging/main armhf pybind11-dev all 2.11.1-1 [191 kB]
Get:127 http://172.17.4.1/private trixie-staging/main armhf libdlib-dev armhf 19.24+dfsg-1 [2006 kB]
Get:128 http://172.17.4.1/private trixie-staging/main armhf libgzstream0 armhf 1.5+git20171107.9a20658-1 [6504 B]
Get:129 http://172.17.4.1/private trixie-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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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
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Setting up libpng16-16:armhf (1.6.40-1) ...
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Setting up dh-autoreconf (20) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libxcb-dri2-0:armhf (1.15-1) ...
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Setting up dwz (0.15-1) ...
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Setting up libllvm15:armhf (1:15.0.6-4+rpi1+b1) ...
Setting up libcurl4:armhf (7.88.1-10+rpi1) ...
Setting up libx11-6:armhf (2:1.8.6-1) ...
Setting up libsuperlu-dev:armhf (6.0.1+dfsg1-1) ...
Setting up libarmadillo12 (1:12.6.1+dfsg-2) ...
Setting up libdrm-amdgpu1:armhf (2.4.115-1+rpi1) ...
Setting up libxcb-dri3-0:armhf (1.15-1) ...
Setting up libx11-xcb1:armhf (2:1.8.6-1) ...
Setting up libdrm-nouveau2:armhf (2.4.115-1+rpi1) ...
Setting up libarpack2-dev:armhf (3.8.0-3) ...
Setting up libdrm-radeon1:armhf (2.4.115-1+rpi1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libgl1-mesa-dri:armhf (23.1.7-1+rpi1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libtbb12:armhf (2021.8.0-2+rpi1) ...
Setting up man-db (2.11.2-3) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libxfixes3:armhf (1:6.0.0-2) ...
Setting up libcurl4-openssl-dev:armhf (7.88.1-10+rpi1) ...
Setting up libhdf5-103-1:armhf (1.10.10+repack-2) ...
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Setting up libtbb-dev:armhf (2021.8.0-2+rpi1) ...
Setting up libhdf5-hl-100:armhf (1.10.10+repack-2) ...
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Setting up libhdf5-hl-cpp-100:armhf (1.10.10+repack-2) ...
Setting up libhdf5-fortran-102:armhf (1.10.10+repack-2) ...
Setting up libhdf5-hl-fortran-100:armhf (1.10.10+repack-2) ...
Setting up libopencv-core406:armhf (4.6.0+dfsg-12+rpi1) ...
Setting up libhdf5-dev (1.10.10+repack-2) ...
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-12+rpi1) ...
Setting up libarmadillo-dev (1:12.6.1+dfsg-2) ...
Processing triggers for sgml-base (1.31) ...
Setting up x11proto-dev (2023.2-1) ...
Setting up libxau-dev:armhf (1:1.0.9-1) ...
Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up libxcb1-dev:armhf (1.15-1) ...
Setting up libx11-dev:armhf (2:1.8.6-1) ...
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_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.137 apt_2.7.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.1 bash_5.2.15-2 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.39.2-1 bsdutils_1:2.39.2-1 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.6 debianutils_5.13 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-4 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+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_0.21-13 gettext-base_0.21-13 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.23.0-2 gzip_1.12-1 hdf5-helpers_1.10.10+repack-2 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-3 libacl1_2.3.1-3 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libarmadillo-dev_1:12.6.1+dfsg-2 libarmadillo12_1:12.6.1+dfsg-2 libarpack2_3.8.0-3 libarpack2-dev_3.8.0-3 libasan8_12.2.0-14+rpi1 libassuan0_2.5.6-1 libatomic1_12.2.0-14+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.40-2+rpi2 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.39.2-1 libboost-dev_1.74.0.3+b4 libboost-program-options-dev_1.74.0.3+b4 libboost-program-options1.74-dev_1.74.0+ds1-22 libboost-program-options1.74.0_1.74.0+ds1-22 libboost1.74-dev_1.74.0+ds1-22 libbrotli1_1.0.9-2+b3 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-9+rpi1+deb12u1 libc-dev-bin_2.36-9+rpi1+deb12u1 libc6_2.36-9+rpi1+deb12u1 libc6-dev_2.36-9+rpi1+deb12u1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_12.2.0-14+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.40-2+rpi2 libctf0_2.40-2+rpi2 libcurl4_7.88.1-10+rpi1 libcurl4-openssl-dev_7.88.1-10+rpi1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.270 libdebhelper-perl_13.11.6 libdlib-data_19.24+dfsg-1 libdlib-dev_19.24+dfsg-1 libdlib19.1_19.24+dfsg-1 libdpkg-perl_1.21.22+rpi1 libdrm-amdgpu1_2.4.115-1+rpi1 libdrm-common_2.4.115-1+rpi1 libdrm-nouveau2_2.4.115-1+rpi1 libdrm-radeon1_2.4.115-1+rpi1 libdrm2_2.4.115-1+rpi1 libedit2_3.1-20230828-1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.2.0-14+rpi1 libgcc-s1_12.2.0-14+rpi1 libgcrypt20_1.10.2-2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-14+rpi1 libgl1-mesa-dri_23.1.7-1+rpi1 libglapi-mesa_23.1.7-1+rpi1 libglvnd0_1.6.0-1 libglx-mesa0_23.1.7-1+rpi1 libglx0_1.6.0-1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_12.2.0-14+rpi1 libgpg-error0_1.47-2 libgssapi-krb5-2_1.20.1-3 libgzstream-dev_1.5+git20171107.9a20658-1 libgzstream0_1.5+git20171107.9a20658-1 libhdf5-103-1_1.10.10+repack-2 libhdf5-cpp-103-1_1.10.10+repack-2 libhdf5-dev_1.10.10+repack-2 libhdf5-fortran-102_1.10.10+repack-2 libhdf5-hl-100_1.10.10+repack-2 libhdf5-hl-cpp-100_1.10.10+repack-2 libhdf5-hl-fortran-100_1.10.10+repack-2 libhogweed6_3.9.1-2 libhwloc15_2.9.3-1 libicu72_72.1-3 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjpeg-dev_1:2.1.5-2 libjpeg62-turbo_1:2.1.5-2 libjpeg62-turbo-dev_1:2.1.5-2 libk5crypto3_1.20.1-3 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-3 libkrb5support0_1.20.1-3 libksba8_1.6.3-2 liblapack-dev_3.11.0-2 liblapack3_3.11.0-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 libllvm15_1:15.0.6-4+rpi1+b1 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncursesw6_6.4+20230625-2 libnettle8_3.9.1-2 libnghttp2-14_1.56.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libopencv-core-dev_4.6.0+dfsg-12+rpi1 libopencv-core406_4.6.0+dfsg-12+rpi1 libp11-kit0_0.25.0-4 libpam-cap_1:2.66-4 libpam-modules_1.5.2-7 libpam-modules-bin_1.5.2-7 libpam-runtime_1.5.2-7 libpam0g_1.5.2-7 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpng-dev_1.6.40-1 libpng16-16_1.6.40-1 libpsl5_0.21.2-1+b1 libpthread-stubs0-dev_0.4-1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.4-1+b2 libsensors-config_1:3.6.0-8 libsensors5_1:3.6.0-8 libsepol1_3.1-1 libsepol2_3.5-1 libsmartcols1_2.39.2-1 libsqlite3-0_3.43.1-1 libsqlite3-dev_3.43.1-1 libss2_1.47.0-2 libssh2-1_1.11.0-2 libssl-dev_3.0.11-1 libssl1.1_1.1.1o-1 libssl3_3.0.11-1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 libsub-override-perl_0.09-4 libsuperlu-dev_6.0.1+dfsg1-1 libsuperlu6_6.0.1+dfsg1-1 libsystemd0_252.12-1~deb12u1+rpi1 libsz2_1.0.6-1 libtasn1-6_4.19.0-3 libtbb-dev_2021.8.0-2+rpi1 libtbb12_2021.8.0-2+rpi1 libtbbbind-2-5_2021.8.0-2+rpi1 libtbbmalloc2_2021.8.0-2+rpi1 libtext-glob-perl_0.11-3 libtinfo6_6.4+20230625-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_12.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_252.12-1~deb12u1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-1 libx11-6_2:1.8.6-1 libx11-data_2:1.8.6-1 libx11-dev_2:1.8.6-1 libx11-xcb1_2:1.8.6-1 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb-dri2-0_1.15-1 libxcb-dri3-0_1.15-1 libxcb-glx0_1.15-1 libxcb-present0_1.15-1 libxcb-randr0_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-1.3 libxshmfence1_1.3-1 libxxf86vm1_1:1.1.4-1+b2 libxxhash0_0.8.1-1 libz3-4_4.8.12-3.1 libzstd1_1.5.5+dfsg2-1 linux-libc-dev_6.1.38-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.11.2-3 mawk_1.3.4.20230808-1 mount_2.39.2-1 nano_7.2-1 ncurses-base_6.4+20230625-2 ncurses-bin_6.4+20230625-2 netbase_6.4 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 pybind11-dev_2.11.1-1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seer-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.07-1 tar_1.34+dfsg-1.2 tzdata_2023c-10 usrmerge_37 util-linux_2.39.2-1 util-linux-extra_2.39.2-1 x11proto-dev_2023.2-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
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 inline signature for ./seer_1.1.4-7.dsc: no acceptable signature found
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
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.1.4-7+b1
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=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-3c0438d5-c1ab-4a8e-b3fa-db87ee74ffc9
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+b1
dpkg-buildpackage: info: source distribution trixie-staging
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
In file included from /usr/include/armadillo:26,
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 seerCommon.o seerCommon.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 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:26,
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:26,
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:26,
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:26,
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:5226:17,
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:522:21,
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:206:14:
/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:5226:17,
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:522:21,
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:206:14:
/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:26,
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/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:1280:25:
/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:26,
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/armadillo:26,
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:26,
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:26,
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:26,
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:26,
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
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
/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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:26,
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")
| ^
In file included from /usr/include/armadillo:26,
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")
| ^
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:26,
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
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 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
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/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/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/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: 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: package could avoid a useless dependency if debian/seer/usr/bin/filter_seer debian/seer/usr/bin/map_back debian/seer/usr/bin/seer debian/seer/usr/bin/combineKmers debian/seer/usr/bin/kmds 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+b1_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.4-7+b1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../seer_1.1.4-7+b1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../seer_1.1.4-7+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-09-27T02:40:03Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.4-7+b1_armhf.changes:
------------------------------
Format: 1.8
Date: Sun, 06 Nov 2022 15:38:02 +0100
Source: seer (1.1.4-7)
Binary: seer seer-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 1.1.4-7+b1
Distribution: trixie-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
seer - genomic sequence element (kmer) enrichment analysis
Changes:
seer (1.1.4-7+b1) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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597255fdd3b7bfe7d075e619b164d1f89b43aaf7 8760 seer_1.1.4-7+b1_armhf.buildinfo
5abf7e07ca40b072be70527068d6cf926db155b9 1066700 seer_1.1.4-7+b1_armhf.deb
Checksums-Sha256:
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efcf4c208f06968d39bdd5779dd22177509f7ce3b5360c1a1cd2155cc77bd2d0 8760 seer_1.1.4-7+b1_armhf.buildinfo
312c8fb16c5cfdc89c4a774119d799311e5ed071ca10d65be774586ddeb7c377 1066700 seer_1.1.4-7+b1_armhf.deb
Files:
b65e403dcdb2f1e5ebc9695714be870c 8674844 debug optional seer-dbgsym_1.1.4-7+b1_armhf.deb
4296d53ee731f3d6c60f6cab21c42a37 8760 science optional seer_1.1.4-7+b1_armhf.buildinfo
4511aa2bdd02c74ab106f233c130fb34 1066700 science optional seer_1.1.4-7+b1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.4-7+b1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 8674844 bytes: control archive=808 bytes.
539 bytes, 12 lines control
614 bytes, 6 lines md5sums
Package: seer-dbgsym
Source: seer (1.1.4-7)
Version: 1.1.4-7+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8939
Depends: seer (= 1.1.4-7+b1)
Section: debug
Priority: optional
Description: debug symbols for seer
Build-Ids: 072413da599cb229cefe40d41cf9ba8585544835 4614bb69a9f1dbc8f7a7ac233cbc3b39a3ff60b0 74a3e6991e1b8a22ac4844cd0615eb4efd67dcf2 c470e402c745f364fb2b35c2ed903a3cc1d6fc15 dedd247bb4d64e06e45bc7b7156f445991b62f38
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/07/
-rw-r--r-- root/root 923012 2022-11-06 14:38 ./usr/lib/debug/.build-id/07/2413da599cb229cefe40d41cf9ba8585544835.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/46/
-rw-r--r-- root/root 481404 2022-11-06 14:38 ./usr/lib/debug/.build-id/46/14bb69a9f1dbc8f7a7ac233cbc3b39a3ff60b0.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/74/
-rw-r--r-- root/root 3443920 2022-11-06 14:38 ./usr/lib/debug/.build-id/74/a3e6991e1b8a22ac4844cd0615eb4efd67dcf2.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/c4/
-rw-r--r-- root/root 2733184 2022-11-06 14:38 ./usr/lib/debug/.build-id/c4/70e402c745f364fb2b35c2ed903a3cc1d6fc15.debug
drwxr-xr-x root/root 0 2022-11-06 14:38 ./usr/lib/debug/.build-id/de/
-rw-r--r-- root/root 392708 2022-11-06 14:38 ./usr/lib/debug/.build-id/de/dd247bb4d64e06e45bc7b7156f445991b62f38.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 1159152 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+b1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 1066700 bytes: control archive=2728 bytes.
1463 bytes, 25 lines control
4405 bytes, 63 lines md5sums
Package: seer
Source: seer (1.1.4-7)
Version: 1.1.4-7+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4419
Depends: libarmadillo12 (>= 1:12.6.1+dfsg), libblas3 | libblas.so.3, libboost-program-options1.74.0 (>= 1.74.0+ds1), 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 79500 2022-11-06 14:38 ./usr/bin/combineKmers
-rwxr-xr-x root/root 63116 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 424076 2022-11-06 14:38 ./usr/bin/kmds
-rwxr-xr-x root/root 145036 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 579756 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 218 2022-11-06 14:38 ./usr/share/doc/seer/changelog.Debian.armhf.gz
-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
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 99988
Build-Time: 498
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 375
Job: seer_1.1.4-7
Machine Architecture: armhf
Package: seer
Package-Time: 898
Source-Version: 1.1.4-7
Space: 99988
Status: successful
Version: 1.1.4-7+b1
--------------------------------------------------------------------------------
Finished at 2023-09-27T02:40:03Z
Build needed 00:14:58, 99988k disk space