seer →
1.1.4-6 →
armhf → 2021-10-16 06:54:30
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| seer 1.1.4-6 (armhf) Sat, 16 Oct 2021 06:30:15 +0000 |
+==============================================================================+
Package: seer
Version: 1.1.4-6
Source Version: 1.1.4-6
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-634b89ed-9c2b-47d7-9477-7eee198fe7bb' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 26s (1013 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 983 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main seer 1.1.4-6 (dsc) [2022 B]
Get:2 http://172.17.0.1/private bookworm-staging/main seer 1.1.4-6 (tar) [972 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main seer 1.1.4-6 (diff) [8532 B]
Fetched 983 kB in 0s (3333 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/seer-X6Ldzp/seer-1.1.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-X6Ldzp' 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-SQHDrF/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-SQHDrF/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-SQHDrF/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2824 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 35 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-SQHDrF/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 (22.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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-SQHDrF/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-SQHDrF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ Sources [536 B]
Get:5 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ Packages [619 B]
Fetched 2488 B in 1s (3280 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gcc-11-base gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarmadillo-dev libarmadillo10 libarpack2
libarpack2-dev libasan6 libatomic1 libblas-dev libblas3 libboost-dev
libboost-program-options-dev libboost-program-options1.74-dev
libboost-program-options1.74.0 libboost1.74-dev libcc1-0 libdebhelper-perl
libdlib-data libdlib-dev libdlib19 libelf1 libfile-stripnondeterminism-perl
libgcc-s1 libgfortran5 libgomp1 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 libicu67 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic-mgc
libmagic1 libpipeline1 libpng16-16 libsigsegv2 libstdc++6
libsub-override-perl libsuperlu-dev libsuperlu5 libsz2 libtool libubsan1
libuchardet0 libxml2 m4 man-db po-debconf sensible-utils 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
libhdf5-doc libsuperlu-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl
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 libarmadillo10 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 libdebhelper-perl
libdlib-data libdlib-dev libdlib19 libelf1 libfile-stripnondeterminism-perl
libgfortran5 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 libicu67 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic-mgc libmagic1
libpipeline1 libpng16-16 libsigsegv2 libsub-override-perl libsuperlu-dev
libsuperlu5 libsz2 libtool libuchardet0 libxml2 m4 man-db po-debconf
sbuild-build-depends-seer-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
gcc-11-base libasan6 libatomic1 libcc1-0 libgcc-s1 libgomp1 libstdc++6
libubsan1
8 upgraded, 69 newly installed, 0 to remove and 27 not upgraded.
Need to get 111 MB of archives.
After this operation, 379 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-SQHDrF/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-3 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-8+rpi1 [1944 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-8+rpi1 [797 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-8+rpi1 [88.1 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-8+rpi1 [205 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-8+rpi1 [36.1 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-8+rpi1 [37.8 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-8+rpi1 [8196 B]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-8+rpi1 [466 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf hdf5-helpers armhf 1.10.7+repack-1 [42.7 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libsz2 armhf 1.0.6-1 [7452 B]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libaec-dev armhf 1.0.6-1 [17.6 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libblas3 armhf 3.10.0-1 [108 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-8+rpi1 [235 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.0-1 [1594 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libarpack2 armhf 3.8.0-1 [85.9 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libsuperlu5 armhf 5.2.2+dfsg1-2 [128 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libarmadillo10 armhf 1:10.6.2+dfsg-1 [98.6 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.0-1 [113 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.0-1 [2872 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libarpack2-dev armhf 3.8.0-1 [94.6 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-103-1 armhf 1.10.7+repack-1 [1232 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-fortran-102 armhf 1.10.7+repack-1 [96.7 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-hl-100 armhf 1.10.7+repack-1 [81.8 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.7+repack-1 [53.5 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.7+repack-1 [132 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.7+repack-1 [39.8 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [122 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.0.6-4 [240 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.0.6-4 [67.8 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-dev armhf 1.10.7+repack-1 [2195 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libsuperlu-dev armhf 5.2.2+dfsg1-2 [21.4 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libarmadillo-dev armhf 1:10.6.2+dfsg-1 [399 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b1 [4820 B]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libboost-program-options1.74.0 armhf 1.74.0-9 [334 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libboost-program-options1.74-dev armhf 1.74.0-9 [374 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libboost-program-options-dev armhf 1.74.0.3+b1 [4616 B]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libdlib-data all 19.10-3.1 [63.4 MB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libdlib19 armhf 19.10-3.1 [3712 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libdlib-dev armhf 19.10-3.1 [1692 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libgzstream0 armhf 1.5+git20171107.9a20658-1 [6504 B]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libgzstream-dev armhf 1.5+git20171107.9a20658-1 [6940 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 111 MB in 13s (8847 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../bsdextrautils_2.37.2-3_armhf.deb ...
Unpacking bsdextrautils (2.37.2-3) ...
Preparing to unpack .../libasan6_11.2.0-8+rpi1_armhf.deb ...
Unpacking libasan6:armhf (11.2.0-8+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libubsan1_11.2.0-8+rpi1_armhf.deb ...
Unpacking libubsan1:armhf (11.2.0-8+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libgomp1_11.2.0-8+rpi1_armhf.deb ...
Unpacking libgomp1:armhf (11.2.0-8+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../gcc-11-base_11.2.0-8+rpi1_armhf.deb ...
Unpacking gcc-11-base:armhf (11.2.0-8+rpi1) over (11.2.0-4+rpi1) ...
Setting up gcc-11-base:armhf (11.2.0-8+rpi1) ...
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../libgcc-s1_11.2.0-8+rpi1_armhf.deb ...
Unpacking libgcc-s1:armhf (11.2.0-8+rpi1) over (11.2.0-4+rpi1) ...
Setting up libgcc-s1:armhf (11.2.0-8+rpi1) ...
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../libcc1-0_11.2.0-8+rpi1_armhf.deb ...
Unpacking libcc1-0:armhf (11.2.0-8+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libatomic1_11.2.0-8+rpi1_armhf.deb ...
Unpacking libatomic1:armhf (11.2.0-8+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libstdc++6_11.2.0-8+rpi1_armhf.deb ...
Unpacking libstdc++6:armhf (11.2.0-8+rpi1) over (11.2.0-4+rpi1) ...
Setting up libstdc++6:armhf (11.2.0-8+rpi1) ...
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../00-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../01-groff-base_1.22.4-7_armhf.deb ...
Unpacking groff-base (1.22.4-7) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../02-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../03-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../04-sensible-utils_0.0.17_all.deb ...
Unpacking sensible-utils (0.0.17) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../05-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../06-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../07-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../08-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../09-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-2_all.deb ...
Unpacking autoconf (2.71-2) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.4-2_all.deb ...
Unpacking automake (1:1.16.4-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.5.2_all.deb ...
Unpacking libdebhelper-perl (13.5.2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../19-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.12.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.12.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../22-libelf1_0.185-2_armhf.deb ...
Unpacking libelf1:armhf (0.185-2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.14-1_armhf.deb ...
Unpacking dwz (0.14-1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../24-libicu67_67.1-7_armhf.deb ...
Unpacking libicu67:armhf (67.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../25-libxml2_2.9.12+dfsg-5_armhf.deb ...
Unpacking libxml2:armhf (2.9.12+dfsg-5) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_13.5.2_all.deb ...
Unpacking debhelper (13.5.2) ...
Selecting previously unselected package hdf5-helpers.
Preparing to unpack .../30-hdf5-helpers_1.10.7+repack-1_armhf.deb ...
Unpacking hdf5-helpers (1.10.7+repack-1) ...
Selecting previously unselected package libaec0:armhf.
Preparing to unpack .../31-libaec0_1.0.6-1_armhf.deb ...
Unpacking libaec0:armhf (1.0.6-1) ...
Selecting previously unselected package libsz2:armhf.
Preparing to unpack .../32-libsz2_1.0.6-1_armhf.deb ...
Unpacking libsz2:armhf (1.0.6-1) ...
Selecting previously unselected package libaec-dev:armhf.
Preparing to unpack .../33-libaec-dev_1.0.6-1_armhf.deb ...
Unpacking libaec-dev:armhf (1.0.6-1) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../34-libblas3_3.10.0-1_armhf.deb ...
Unpacking libblas3:armhf (3.10.0-1) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../35-libgfortran5_11.2.0-8+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (11.2.0-8+rpi1) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../36-liblapack3_3.10.0-1_armhf.deb ...
Unpacking liblapack3:armhf (3.10.0-1) ...
Selecting previously unselected package libarpack2:armhf.
Preparing to unpack .../37-libarpack2_3.8.0-1_armhf.deb ...
Unpacking libarpack2:armhf (3.8.0-1) ...
Selecting previously unselected package libsuperlu5:armhf.
Preparing to unpack .../38-libsuperlu5_5.2.2+dfsg1-2_armhf.deb ...
Unpacking libsuperlu5:armhf (5.2.2+dfsg1-2) ...
Selecting previously unselected package libarmadillo10.
Preparing to unpack .../39-libarmadillo10_1%3a10.6.2+dfsg-1_armhf.deb ...
Unpacking libarmadillo10 (1:10.6.2+dfsg-1) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../40-libblas-dev_3.10.0-1_armhf.deb ...
Unpacking libblas-dev:armhf (3.10.0-1) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../41-liblapack-dev_3.10.0-1_armhf.deb ...
Unpacking liblapack-dev:armhf (3.10.0-1) ...
Selecting previously unselected package libarpack2-dev:armhf.
Preparing to unpack .../42-libarpack2-dev_3.8.0-1_armhf.deb ...
Unpacking libarpack2-dev:armhf (3.8.0-1) ...
Selecting previously unselected package libhdf5-103-1:armhf.
Preparing to unpack .../43-libhdf5-103-1_1.10.7+repack-1_armhf.deb ...
Unpacking libhdf5-103-1:armhf (1.10.7+repack-1) ...
Selecting previously unselected package libhdf5-fortran-102:armhf.
Preparing to unpack .../44-libhdf5-fortran-102_1.10.7+repack-1_armhf.deb ...
Unpacking libhdf5-fortran-102:armhf (1.10.7+repack-1) ...
Selecting previously unselected package libhdf5-hl-100:armhf.
Preparing to unpack .../45-libhdf5-hl-100_1.10.7+repack-1_armhf.deb ...
Unpacking libhdf5-hl-100:armhf (1.10.7+repack-1) ...
Selecting previously unselected package libhdf5-hl-fortran-100:armhf.
Preparing to unpack .../46-libhdf5-hl-fortran-100_1.10.7+repack-1_armhf.deb ...
Unpacking libhdf5-hl-fortran-100:armhf (1.10.7+repack-1) ...
Selecting previously unselected package libhdf5-cpp-103-1:armhf.
Preparing to unpack .../47-libhdf5-cpp-103-1_1.10.7+repack-1_armhf.deb ...
Unpacking libhdf5-cpp-103-1:armhf (1.10.7+repack-1) ...
Selecting previously unselected package libhdf5-hl-cpp-100:armhf.
Preparing to unpack .../48-libhdf5-hl-cpp-100_1.10.7+repack-1_armhf.deb ...
Unpacking libhdf5-hl-cpp-100:armhf (1.10.7+repack-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../49-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../50-libjpeg62-turbo_1%3a2.0.6-4_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:2.0.6-4) ...
Selecting previously unselected package libjpeg62-turbo-dev:armhf.
Preparing to unpack .../51-libjpeg62-turbo-dev_1%3a2.0.6-4_armhf.deb ...
Unpacking libjpeg62-turbo-dev:armhf (1:2.0.6-4) ...
Selecting previously unselected package libjpeg-dev:armhf.
Preparing to unpack .../52-libjpeg-dev_1%3a2.0.6-4_armhf.deb ...
Unpacking libjpeg-dev:armhf (1:2.0.6-4) ...
Selecting previously unselected package libhdf5-dev.
Preparing to unpack .../53-libhdf5-dev_1.10.7+repack-1_armhf.deb ...
Unpacking libhdf5-dev (1.10.7+repack-1) ...
Selecting previously unselected package libsuperlu-dev:armhf.
Preparing to unpack .../54-libsuperlu-dev_5.2.2+dfsg1-2_armhf.deb ...
Unpacking libsuperlu-dev:armhf (5.2.2+dfsg1-2) ...
Selecting previously unselected package libarmadillo-dev.
Preparing to unpack .../55-libarmadillo-dev_1%3a10.6.2+dfsg-1_armhf.deb ...
Unpacking libarmadillo-dev (1:10.6.2+dfsg-1) ...
Selecting previously unselected package libboost1.74-dev:armhf.
Preparing to unpack .../56-libboost1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../57-libboost-dev_1.74.0.3+b1_armhf.deb ...
Unpacking libboost-dev:armhf (1.74.0.3+b1) ...
Selecting previously unselected package libboost-program-options1.74.0:armhf.
Preparing to unpack .../58-libboost-program-options1.74.0_1.74.0-9_armhf.deb ...
Unpacking libboost-program-options1.74.0:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-program-options1.74-dev:armhf.
Preparing to unpack .../59-libboost-program-options1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost-program-options1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-program-options-dev:armhf.
Preparing to unpack .../60-libboost-program-options-dev_1.74.0.3+b1_armhf.deb ...
Unpacking libboost-program-options-dev:armhf (1.74.0.3+b1) ...
Selecting previously unselected package libdlib-data.
Preparing to unpack .../61-libdlib-data_19.10-3.1_all.deb ...
Unpacking libdlib-data (19.10-3.1) ...
Selecting previously unselected package libpng16-16:armhf.
Preparing to unpack .../62-libpng16-16_1.6.37-3_armhf.deb ...
Unpacking libpng16-16:armhf (1.6.37-3) ...
Selecting previously unselected package libdlib19:armhf.
Preparing to unpack .../63-libdlib19_19.10-3.1_armhf.deb ...
Unpacking libdlib19:armhf (19.10-3.1) ...
Selecting previously unselected package libdlib-dev:armhf.
Preparing to unpack .../64-libdlib-dev_19.10-3.1_armhf.deb ...
Unpacking libdlib-dev:armhf (19.10-3.1) ...
Selecting previously unselected package libgzstream0:armhf.
Preparing to unpack .../65-libgzstream0_1.5+git20171107.9a20658-1_armhf.deb ...
Unpacking libgzstream0:armhf (1.5+git20171107.9a20658-1) ...
Selecting previously unselected package libgzstream-dev:armhf.
Preparing to unpack .../66-libgzstream-dev_1.5+git20171107.9a20658-1_armhf.deb ...
Unpacking libgzstream-dev:armhf (1.5+git20171107.9a20658-1) ...
Selecting previously unselected package sbuild-build-depends-seer-dummy.
Preparing to unpack .../67-sbuild-build-depends-seer-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-seer-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libboost1.74-dev:armhf (1.74.0-9) ...
Setting up bsdextrautils (2.37.2-3) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up hdf5-helpers (1.10.7+repack-1) ...
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libboost-program-options1.74.0:armhf (1.74.0-9) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libgomp1:armhf (11.2.0-8+rpi1) ...
Setting up libaec0:armhf (1.0.6-1) ...
Setting up libasan6:armhf (11.2.0-8+rpi1) ...
Setting up libboost-program-options1.74-dev:armhf (1.74.0-9) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libblas3:armhf (3.10.0-1) ...
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
Setting up libjpeg62-turbo:armhf (1:2.0.6-4) ...
Setting up libboost-program-options-dev:armhf (1.74.0.3+b1) ...
Setting up libjpeg62-turbo-dev:armhf (1:2.0.6-4) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libpng16-16:armhf (1.6.37-3) ...
Setting up libatomic1:armhf (11.2.0-8+rpi1) ...
Setting up autopoint (0.21-4) ...
Setting up libgfortran5:armhf (11.2.0-8+rpi1) ...
Setting up libgzstream0:armhf (1.5+git20171107.9a20658-1) ...
Setting up libubsan1:armhf (11.2.0-8+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libboost-dev:armhf (1.74.0.3+b1) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libdlib-data (19.10-3.1) ...
Setting up libcc1-0:armhf (11.2.0-8+rpi1) ...
Setting up libblas-dev:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libsz2:armhf (1.0.6-1) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up liblapack3:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up libaec-dev:armhf (1.0.6-1) ...
Setting up libarpack2:armhf (3.8.0-1) ...
Setting up libjpeg-dev:armhf (1:2.0.6-4) ...
Setting up libsuperlu5:armhf (5.2.2+dfsg1-2) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libgzstream-dev:armhf (1.5+git20171107.9a20658-1) ...
Setting up libdlib19:armhf (19.10-3.1) ...
Setting up liblapack-dev:armhf (3.10.0-1) ...
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 autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up libhdf5-103-1:armhf (1.10.7+repack-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up libhdf5-cpp-103-1:armhf (1.10.7+repack-1) ...
Setting up libsuperlu-dev:armhf (5.2.2+dfsg1-2) ...
Setting up libhdf5-hl-100:armhf (1.10.7+repack-1) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libarmadillo10 (1:10.6.2+dfsg-1) ...
Setting up libarpack2-dev:armhf (3.8.0-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libdlib-dev:armhf (19.10-3.1) ...
Setting up dh-autoreconf (20) ...
Setting up libhdf5-hl-cpp-100:armhf (1.10.7+repack-1) ...
Setting up libhdf5-fortran-102:armhf (1.10.7+repack-1) ...
Setting up libhdf5-hl-fortran-100:armhf (1.10.7+repack-1) ...
Setting up debhelper (13.5.2) ...
Setting up libhdf5-dev (1.10.7+repack-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libarmadillo-dev (1:10.6.2+dfsg-1) ...
Setting up sbuild-build-depends-seer-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-8+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-3 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-8+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_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hdf5-helpers_1.10.7+repack-1 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libarmadillo-dev_1:10.6.2+dfsg-1 libarmadillo10_1:10.6.2+dfsg-1 libarpack2_3.8.0-1 libarpack2-dev_3.8.0-1 libasan6_11.2.0-8+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-8+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblas-dev_3.10.0-1 libblas3_3.10.0-1 libblkid1_2.37.2-1 libboost-dev_1.74.0.3+b1 libboost-program-options-dev_1.74.0.3+b1 libboost-program-options1.74-dev_1.74.0-9 libboost-program-options1.74.0_1.74.0-9 libboost1.74-dev_1.74.0-9 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-8+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdlib-data_19.10-3.1 libdlib-dev_19.10-3.1 libdlib19_19.10-3.1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-8+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgfortran5_11.2.0-8+rpi1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-8+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libgzstream-dev_1.5+git20171107.9a20658-1 libgzstream0_1.5+git20171107.9a20658-1 libhdf5-103-1_1.10.7+repack-1 libhdf5-cpp-103-1_1.10.7+repack-1 libhdf5-dev_1.10.7+repack-1 libhdf5-fortran-102_1.10.7+repack-1 libhdf5-hl-100_1.10.7+repack-1 libhdf5-hl-cpp-100_1.10.7+repack-1 libhdf5-hl-fortran-100_1.10.7+repack-1 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libjpeg-dev_1:2.0.6-4 libjpeg62-turbo_1:2.0.6-4 libjpeg62-turbo-dev_1:2.0.6-4 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack-dev_3.10.0-1 liblapack3_3.10.0-1 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-8+rpi1 libsub-override-perl_0.09-2 libsuperlu-dev_5.2.2+dfsg1-2 libsuperlu5_5.2.2+dfsg1-2 libsystemd0_247.9-1+rpi1 libsz2_1.0.6-1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-8+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seer-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.ohr0bk7Z/trustedkeys.kbx': General error
gpgv: Signature made Wed Oct 13 20:24:16 2021 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./seer_1.1.4-6.dsc
dpkg-source: info: extracting seer in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking seer_1.1.4.orig.tar.gz
dpkg-source: info: unpacking seer_1.1.4-6.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
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-634b89ed-9c2b-47d7-9477-7eee198fe7bb
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package seer
dpkg-buildpackage: info: source version 1.1.4-6
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -f *.o ~* seer kmds map_back combineKmers filter_seer
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
cd test && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
rm -f *.o ~* tests_passed
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- LDFLAGS+=-L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make -j4 "INSTALL=install --strip-program=true" LDFLAGS\+=-L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o sample.o sample.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o significant_kmer.o significant_kmer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmer.o kmer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o covar.o covar.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCommon.o seerCommon.cpp
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
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
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)
| ~~^~~~~~~~~~~~~~~
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
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++/10/bits/stl_algobase.h:71,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/ios:40,
from /usr/include/c++/10/ostream:38,
from /usr/include/c++/10/iostream:39,
from seercommon.hpp:10,
from seerIO.cpp:12:
/usr/include/c++/10/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++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
155 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/10/bits/predefined_ops.h:155:9: 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++/10/vector:72,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sample&}; _Tp = Sample; _Alloc = std::allocator<Sample>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sample>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/10/bits/stl_vector.h: In function 'static bool arma::diskio::save_hdf5_binary(const arma::Mat<eT>&, const arma::hdf5_name&, std::string&) [with eT = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Distance = int; _Tp = Sample; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(Sample, Sample)>]':
/usr/include/c++/10/bits/stl_heap.h:134:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
134 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Distance = int; _Tp = Sample; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:82:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
82 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:84:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
84 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:86:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:91:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
91 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/10/bits/stl_vector.h: In function 'void readPheno(const string&, std::vector<Sample>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Kmer&}; _Tp = Kmer; _Alloc = std::allocator<Kmer>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Kmer>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
1198 | _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
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/c++/10/vector:72,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' 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 kmdsMain.o kmdsMain.cpp
In file included from /usr/include/c++/10/vector:72,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const arma::Col<double>&}; _Tp = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: 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++/10/vector:67,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/c++/10/bits/stl_vector.h: In function 'void doLinear(Kmer&, const vec&, const mat&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/c++/10/bits/stl_vector.h: In function 'void newtonRaphson(Kmer&, const vec&, const mat&, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void doLogit(Kmer&, const vec&, const mat&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _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 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
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
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++/10/vector:72,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DistanceElement&}; _Tp = DistanceElement; _Alloc = std::allocator<DistanceElement>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<DistanceElement>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<DistanceElement>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/c++/10/bits/stl_vector.h: In function 'arma::mat dissimiliarityMatrix(const mat&, unsigned int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DistanceElement*, std::vector<DistanceElement> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsMain.cpp:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {arma::Col<double>}; _Tp = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<arma::Col<double> >::iterator' changed in GCC 7.1
426 | 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
/usr/include/c++/10/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
121 | _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++/10/list:63,
from filter_seer.hpp:11,
from filter_seer.cpp:7:
/usr/include/c++/10/bits/stl_list.h: In member function 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(std::__cxx11::list<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Significant_kmer&}; _Tp = Significant_kmer; _Alloc = std::allocator<Significant_kmer>]':
/usr/include/c++/10/bits/stl_list.h:1909:8: note: parameter passing for argument of type 'std::__cxx11::list<Significant_kmer>::iterator' changed in GCC 7.1
1909 | _M_insert(iterator __position, _Args&&... __args)
| ^~~~~~~~~
/usr/include/c++/10/bits/stl_list.h: In function 'int main(int, char**)':
/usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type 'std::_List_iterator<Significant_kmer>' changed in GCC 7.1
1212 | { 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/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/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/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/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/combineKmers was not linked against libz.so.1 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/seer debian/seer/usr/bin/map_back debian/seer/usr/bin/combineKmers debian/seer/usr/bin/filter_seer debian/seer/usr/bin/kmds were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'seer-dbgsym' in '../seer-dbgsym_1.1.4-6_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.4-6_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../seer_1.1.4-6_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 2021-10-16T06:54:10Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.4-6_armhf.changes:
---------------------------
Format: 1.8
Date: Wed, 13 Oct 2021 22:10:45 +0200
Source: seer
Binary: seer seer-dbgsym
Architecture: armhf
Version: 1.1.4-6
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
seer - genomic sequence element (kmer) enrichment analysis
Changes:
seer (1.1.4-6) unstable; urgency=medium
.
* Team upload.
* Fix watchfile to detect new versions on github
* Standards-Version: 4.6.0 (routine-update)
Checksums-Sha1:
d0422bd35c5e3d53d8a5a2dead09663d9383cfb0 8534448 seer-dbgsym_1.1.4-6_armhf.deb
320095d9167c24049d10a636ec5fd1e43898ab38 6068 seer_1.1.4-6_armhf.buildinfo
38c75346b30a64db4ca83d8768e59525b889d694 1066256 seer_1.1.4-6_armhf.deb
Checksums-Sha256:
5d8c57489803e6e316ba55d1fab167d8ff0a03ba17e8e4de5d26f04f676fa233 8534448 seer-dbgsym_1.1.4-6_armhf.deb
3ac789684d16f8c57910def4454a8d2b3e98c844aab0d3ba43bc58233636319c 6068 seer_1.1.4-6_armhf.buildinfo
e8a67b84521fc1c1abbf9ecf0435bf8e6ed9a65687fe1da49068f57d5c6b397c 1066256 seer_1.1.4-6_armhf.deb
Files:
6e374347bcc9e0d8ac1e2b75a494fd83 8534448 debug optional seer-dbgsym_1.1.4-6_armhf.deb
2555139a0aa4b4755324bd55b7d912a0 6068 science optional seer_1.1.4-6_armhf.buildinfo
84496d1234f477d1118d7fd2c86b79a1 1066256 science optional seer_1.1.4-6_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.4-6_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 8534448 bytes: control archive=800 bytes.
523 bytes, 12 lines control
614 bytes, 6 lines md5sums
Package: seer-dbgsym
Source: seer
Version: 1.1.4-6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8845
Depends: seer (= 1.1.4-6)
Section: debug
Priority: optional
Description: debug symbols for seer
Build-Ids: 5e338b5d8032c362b057e51dbaf24f9febda2e71 b3c143e1a3ed2c52db64215dd72bd73b0f876c78 f12386be21fa080846a869c0bc8d7076a3d111d4 f135c7787828ac38bec111494541784b3b4d779a fe9f9f14a3d9ae2f502492037b8a4e03907dcdc1
drwxr-xr-x root/root 0 2021-10-13 20:10 ./
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/lib/debug/.build-id/5e/
-rw-r--r-- root/root 1015620 2021-10-13 20:10 ./usr/lib/debug/.build-id/5e/338b5d8032c362b057e51dbaf24f9febda2e71.debug
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/lib/debug/.build-id/b3/
-rw-r--r-- root/root 367008 2021-10-13 20:10 ./usr/lib/debug/.build-id/b3/c143e1a3ed2c52db64215dd72bd73b0f876c78.debug
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/lib/debug/.build-id/f1/
-rw-r--r-- root/root 3353880 2021-10-13 20:10 ./usr/lib/debug/.build-id/f1/2386be21fa080846a869c0bc8d7076a3d111d4.debug
-rw-r--r-- root/root 2786424 2021-10-13 20:10 ./usr/lib/debug/.build-id/f1/35c7787828ac38bec111494541784b3b4d779a.debug
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/lib/debug/.build-id/fe/
-rw-r--r-- root/root 467112 2021-10-13 20:10 ./usr/lib/debug/.build-id/fe/9f9f14a3d9ae2f502492037b8a4e03907dcdc1.debug
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 1048372 2021-10-13 20:10 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/seer.debug
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/share/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-13 20:10 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.4-6_armhf.deb
----------------------
new Debian package, version 2.0.
size 1066256 bytes: control archive=2660 bytes.
1432 bytes, 24 lines control
4248 bytes, 61 lines md5sums
Package: seer
Version: 1.1.4-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4433
Depends: libarmadillo10 (>= 1:10.6.2+dfsg), libblas3 | libblas.so.3, libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgzstream0 (>= 1.5+dfsg), libhdf5-103-1, libstdc++6 (>= 7), 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 2021-10-13 20:10 ./
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/bin/
-rwxr-xr-x root/root 4597 2021-10-13 20:10 ./usr/bin/R_mds
-rwxr-xr-x root/root 3794 2021-10-13 20:10 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 2152 2021-10-13 20:10 ./usr/bin/blastn_to_phandango
-rwxr-xr-x root/root 79500 2021-10-13 20:10 ./usr/bin/combineKmers
-rwxr-xr-x root/root 67212 2021-10-13 20:10 ./usr/bin/filter_seer
-rwxr-xr-x root/root 1869 2021-10-13 20:10 ./usr/bin/hits_to_fastq
-rwxr-xr-x root/root 419980 2021-10-13 20:10 ./usr/bin/kmds
-rwxr-xr-x root/root 161420 2021-10-13 20:10 ./usr/bin/map_back
-rwxr-xr-x root/root 3200 2021-10-13 20:10 ./usr/bin/mapping_to_phandango
-rwxr-xr-x root/root 1208 2021-10-13 20:10 ./usr/bin/mash2matrix
-rwxr-xr-x root/root 2295 2021-10-13 20:10 ./usr/bin/reformat_output
-rwxr-xr-x root/root 579756 2021-10-13 20:10 ./usr/bin/seer
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/share/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/share/doc/seer/
-rw-r--r-- root/root 684 2021-10-13 20:08 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 328 2021-10-13 20:08 ./usr/share/doc/seer/README.source
-rw-r--r-- root/root 278 2021-10-13 20:08 ./usr/share/doc/seer/README.test
-rw-r--r-- root/root 1153 2021-10-13 20:10 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1009 2021-10-13 20:08 ./usr/share/doc/seer/copyright
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/share/doc/seer/examples/
-rw-r--r-- root/root 2168438 2017-06-20 09:43 ./usr/share/doc/seer/examples/6259_5_16.fa
-rw-r--r-- root/root 121 2017-06-20 09:43 ./usr/share/doc/seer/examples/Makefile
-rw-r--r-- root/root 196442 2017-06-20 09:43 ./usr/share/doc/seer/examples/all_structure_new
-rw-r--r-- root/root 29617 2017-06-20 09:43 ./usr/share/doc/seer/examples/all_structure_new.samples
-rw-r--r-- root/root 23 2017-06-20 09:43 ./usr/share/doc/seer/examples/assembly_locations.txt
-rw-r--r-- root/root 3011 2017-06-20 09:43 ./usr/share/doc/seer/examples/covariates.txt
-rw-r--r-- root/root 65372 2017-06-20 09:43 ./usr/share/doc/seer/examples/example.pheno
-rw-r--r-- root/root 63448 2021-10-13 20:10 ./usr/share/doc/seer/examples/example_kmers.gz
-rwxr-xr-x root/root 6542 2017-06-20 09:43 ./usr/share/doc/seer/examples/example_wrapper.py
-rw-r--r-- root/root 18732 2017-06-20 09:43 ./usr/share/doc/seer/examples/filter_in.txt
-rwxr-xr-x root/root 1115 2017-06-20 09:43 ./usr/share/doc/seer/examples/generate_test.pl
-rw-r--r-- root/root 233 2017-06-20 09:43 ./usr/share/doc/seer/examples/map_in.txt
-rwxr-xr-x root/root 2031 2017-06-20 09:43 ./usr/share/doc/seer/examples/run_test.pl
-rw-r--r-- root/root 4530 2017-06-20 09:43 ./usr/share/doc/seer/examples/subset.cont.pheno
-rw-r--r-- root/root 4238 2017-06-20 09:43 ./usr/share/doc/seer/examples/subset.pheno
-rw-r--r-- root/root 168 2017-06-20 09:43 ./usr/share/doc/seer/examples/test1.e.txt
-rw-r--r-- root/root 63 2017-06-20 09:43 ./usr/share/doc/seer/examples/test1.o.txt
-rw-r--r-- root/root 171 2017-06-20 09:43 ./usr/share/doc/seer/examples/test2.e.txt
-rw-r--r-- root/root 18732 2017-06-20 09:43 ./usr/share/doc/seer/examples/test2.o.txt
-rw-r--r-- root/root 170 2017-06-20 09:43 ./usr/share/doc/seer/examples/test3.e.txt
-rw-r--r-- root/root 496392 2017-06-20 09:43 ./usr/share/doc/seer/examples/test3.o.txt
-rw-r--r-- root/root 174 2017-06-20 09:43 ./usr/share/doc/seer/examples/test4.e.txt
-rw-r--r-- root/root 9798 2017-06-20 09:43 ./usr/share/doc/seer/examples/test4.o.txt
-rw-r--r-- root/root 171 2017-06-20 09:43 ./usr/share/doc/seer/examples/test5.e.txt
-rw-r--r-- root/root 24941 2017-06-20 09:43 ./usr/share/doc/seer/examples/test5.o.txt
-rw-r--r-- root/root 171 2017-06-20 09:43 ./usr/share/doc/seer/examples/test6.e.txt
-rw-r--r-- root/root 24672 2017-06-20 09:43 ./usr/share/doc/seer/examples/test6.o.txt
-rw-r--r-- root/root 55 2017-06-20 09:43 ./usr/share/doc/seer/examples/test7.e.txt
-rw-r--r-- root/root 15565 2017-06-20 09:43 ./usr/share/doc/seer/examples/test7.o.txt
-rw-r--r-- root/root 121 2017-06-20 09:43 ./usr/share/doc/seer/examples/test8.e.txt
-rw-r--r-- root/root 62 2017-06-20 09:43 ./usr/share/doc/seer/examples/test8.o.txt
-rw-r--r-- root/root 0 2021-10-13 20:10 ./usr/share/doc/seer/examples/tests_passed
-rw-r--r-- root/root 1803 2021-10-13 20:08 ./usr/share/doc/seer/run-unit-test
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-13 20:10 ./usr/share/man/man1/
-rw-r--r-- root/root 506 2021-10-13 20:10 ./usr/share/man/man1/R_mds.1.gz
-rw-r--r-- root/root 501 2021-10-13 20:10 ./usr/share/man/man1/blast_top_hits.1.gz
-rw-r--r-- root/root 461 2021-10-13 20:10 ./usr/share/man/man1/combineKmers.1.gz
-rw-r--r-- root/root 543 2021-10-13 20:10 ./usr/share/man/man1/filter_seer.1.gz
-rw-r--r-- root/root 408 2021-10-13 20:10 ./usr/share/man/man1/hits_to_fastq.1.gz
-rw-r--r-- root/root 906 2021-10-13 20:10 ./usr/share/man/man1/kmds.1.gz
-rw-r--r-- root/root 458 2021-10-13 20:10 ./usr/share/man/man1/map_back.1.gz
-rw-r--r-- root/root 432 2021-10-13 20:10 ./usr/share/man/man1/mapping_to_phandango.1.gz
-rw-r--r-- root/root 466 2021-10-13 20:10 ./usr/share/man/man1/mash2matrix.1.gz
-rw-r--r-- root/root 422 2021-10-13 20:10 ./usr/share/man/man1/reformat_output.1.gz
-rw-r--r-- root/root 995 2021-10-13 20:10 ./usr/share/man/man1/seer.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 110872
Build-Time: 944
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 441
Job: seer_1.1.4-6
Machine Architecture: armhf
Package: seer
Package-Time: 1435
Source-Version: 1.1.4-6
Space: 110872
Status: successful
Version: 1.1.4-6
--------------------------------------------------------------------------------
Finished at 2021-10-16T06:54:10Z
Build needed 00:23:55, 110872k disc space