seer →
1.1.4-3 →
armhf → 2020-06-04 18:24:25
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| seer 1.1.4-3 (armhf) Thu, 04 Jun 2020 18:01:00 +0000 |
+==============================================================================+
Package: seer
Version: 1.1.4-3
Source Version: 1.1.4-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-1e93d5b9-87de-45b9-8fde-283e57c3fcf7' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 27s (910 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 982 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main seer 1.1.4-3 (dsc) [2041 B]
Get:2 http://172.17.0.1/private bullseye-staging/main seer 1.1.4-3 (tar) [972 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main seer 1.1.4-3 (diff) [8156 B]
Fetched 982 kB in 0s (2046 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/seer-2yMgiP/seer-1.1.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-2yMgiP' 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-ZJUIvc/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-ZJUIvc/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ZJUIvc/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-ZJUIvc/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2868 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 7 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (23.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12213 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 (>= 1:6.700.6+dfsg-1~), libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev
Filtered Build-Depends: debhelper-compat (= 13), libarmadillo-dev (>= 1:6.700.6+dfsg-1~), libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev
dpkg-deb: building package 'sbuild-build-depends-seer-dummy' in '/<<BUILDDIR>>/resolver-ZJUIvc/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-ZJUIvc/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ Sources [556 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ Packages [636 B]
Fetched 2525 B in 1s (3399 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 bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gcc-10-base gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarmadillo-dev libarmadillo9 libarpack2 libarpack2-dev
libatomic1 libblas-dev libblas3 libboost-dev libboost-program-options-dev
libboost-program-options1.67-dev libboost-program-options1.67.0
libboost1.67-dev libbsd0 libcc1-0 libcroco3 libdebhelper-perl libdlib-data
libdlib-dev libdlib19 libelf1 libfile-stripnondeterminism-perl libgcc-s1
libgfortran5 libglib2.0-0 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 libicu63
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 libtinfo5 libtool
libubsan1 libuchardet0 libxml2 m4 man-db po-debconf sensible-utils
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libitpp-dev liblapack-doc libboost-doc libboost1.67-doc
libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev
libboost-context1.67-dev libboost-contract1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-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 libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils 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 libarmadillo9 libarpack2 libarpack2-dev
libblas-dev libblas3 libboost-dev libboost-program-options-dev
libboost-program-options1.67-dev libboost-program-options1.67.0
libboost1.67-dev libbsd0 libcroco3 libdebhelper-perl libdlib-data
libdlib-dev libdlib19 libelf1 libfile-stripnondeterminism-perl libgfortran5
libglib2.0-0 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 libicu63 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic-mgc libmagic1
libpipeline1 libpng16-16 libsigsegv2 libsub-override-perl libsuperlu-dev
libsuperlu5 libsz2 libtinfo5 libtool libuchardet0 libxml2 m4 man-db
po-debconf sbuild-build-depends-seer-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
gcc-10-base libatomic1 libcc1-0 libgcc-s1 libgomp1 libstdc++6 libubsan1
7 upgraded, 73 newly installed, 0 to remove and 0 not upgraded.
Need to get 108 MB of archives.
After this operation, 372 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ZJUIvc/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 10.1.0-2+rpi1 [8172 B]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 10.1.0-2+rpi1 [115 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 10.1.0-2+rpi1 [82.9 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10.1.0-2+rpi1 [197 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10.1.0-2+rpi1 [36.1 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.1.0-2+rpi1 [31.7 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 10.1.0-2+rpi1 [408 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.1 [187 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [25.2 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.1-1 [14.9 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.2-1 [1158 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5 [592 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.1 [1012 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf hdf5-helpers armhf 1.10.6+repack-2 [40.0 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libaec0 armhf 1.0.4-1 [20.0 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libsz2 armhf 1.0.4-1 [6664 B]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libaec-dev armhf 1.0.4-1 [17.8 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-2 [108 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-2+rpi1 [232 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-2 [1602 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libarpack2 armhf 3.7.0-3 [85.7 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libsuperlu5 armhf 5.2.1+dfsg1-4 [126 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libarmadillo9 armhf 1:9.800.4+dfsg-1 [93.4 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-2 [113 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-2 [2981 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libarpack2-dev armhf 3.7.0-3 [96.2 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-103-1 armhf 1.10.6+repack-2 [1184 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-fortran-102 armhf 1.10.6+repack-2 [93.0 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-100 armhf 1.10.6+repack-2 [78.1 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.6+repack-2 [49.8 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.6+repack-2 [128 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.6+repack-2 [36.9 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-dev armhf 1.10.6+repack-2 [2167 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-4 [18.4 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libarmadillo-dev armhf 1:9.800.4+dfsg-1 [379 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-18 [8389 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b12 [4464 B]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.67.0 armhf 1.67.0-18 [333 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.67-dev armhf 1.67.0-18 [378 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options-dev armhf 1.67.0.2+b12 [4260 B]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libdlib-data all 19.10-3 [63.4 MB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-2 [274 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libdlib19 armhf 19.10-3 [3717 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libdlib-dev armhf 19.10-3 [1694 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libgzstream0 armhf 1.5+dfsg-4 [6092 B]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libgzstream-dev armhf 1.5+dfsg-4 [6536 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 108 MB in 34s (3157 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 12213 files and directories currently installed.)
Preparing to unpack .../0-libbsd0_0.10.0-1_armhf.deb ...
Unpacking libbsd0:armhf (0.10.0-1) ...
Selecting previously unselected package libtinfo5:armhf.
Preparing to unpack .../1-libtinfo5_6.2-1_armhf.deb ...
Unpacking libtinfo5:armhf (6.2-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../2-bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Preparing to unpack .../3-libatomic1_10.1.0-2+rpi1_armhf.deb ...
Unpacking libatomic1:armhf (10.1.0-2+rpi1) over (10.1.0-1+rpi1) ...
Preparing to unpack .../4-libubsan1_10.1.0-2+rpi1_armhf.deb ...
Unpacking libubsan1:armhf (10.1.0-2+rpi1) over (10.1.0-1+rpi1) ...
Preparing to unpack .../5-libgomp1_10.1.0-2+rpi1_armhf.deb ...
Unpacking libgomp1:armhf (10.1.0-2+rpi1) over (10.1.0-1+rpi1) ...
Preparing to unpack .../6-gcc-10-base_10.1.0-2+rpi1_armhf.deb ...
Unpacking gcc-10-base:armhf (10.1.0-2+rpi1) over (10.1.0-1+rpi1) ...
Setting up gcc-10-base:armhf (10.1.0-2+rpi1) ...
(Reading database ... 12346 files and directories currently installed.)
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Setting up libarmadillo-dev (1:9.800.4+dfsg-1) ...
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Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-13+rpi1 gcc-9_9.3.0-13+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-13+rpi1 libstdc++6_10.1.0-2+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.5 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.35.2-2 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-13+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-13+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-2+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-4+rpi1 gcc-9_9.3.0-13+rpi1 gcc-9-base_9.3.0-13+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hdf5-helpers_1.10.6+repack-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg6.0_2.1.5 libarchive-zip-perl_1.68-1 libarmadillo-dev_1:9.800.4+dfsg-1 libarmadillo9_1:9.800.4+dfsg-1 libarpack2_3.7.0-3 libarpack2-dev_3.7.0-3 libasan5_9.3.0-13+rpi1 libassuan0_2.5.3-7 libatomic1_10.1.0-2+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblas-dev_3.9.0-2 libblas3_3.9.0-2 libblkid1_2.35.2-2 libboost-dev_1.67.0.2+b12 libboost-program-options-dev_1.67.0.2+b12 libboost-program-options1.67-dev_1.67.0-18 libboost-program-options1.67.0_1.67.0-18 libboost1.67-dev_1.67.0-18 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10.1.0-2+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.1 libdlib-data_19.10-3 libdlib-dev_19.10-3 libdlib19_19.10-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libgcc-9-dev_9.3.0-13+rpi1 libgcc-s1_10.1.0-2+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10.1.0-2+rpi1 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10.1.0-2+rpi1 libgpg-error0_1.37-1 libgzstream-dev_1.5+dfsg-4 libgzstream0_1.5+dfsg-4 libhdf5-103-1_1.10.6+repack-2 libhdf5-cpp-103-1_1.10.6+repack-2 libhdf5-dev_1.10.6+repack-2 libhdf5-fortran-102_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhdf5-hl-cpp-100_1.10.6+repack-2 libhdf5-hl-fortran-100_1.10.6+repack-2 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libksba8_1.3.5-2 liblapack-dev_3.9.0-2 liblapack3_3.9.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.2-1 libpipeline1_1.5.2-2 libpng16-16_1.6.37-2 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-2 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libstdc++-9-dev_9.3.0-13+rpi1 libstdc++6_10.1.0-2+rpi1 libsub-override-perl_0.09-2 libsuperlu-dev_5.2.1+dfsg1-4 libsuperlu5_5.2.1+dfsg1-4 libsystemd0_245.5-3+rpi1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-2+rpi1 libuchardet0_0.0.6-3 libudev1_245.5-3+rpi1 libunistring2_0.9.10-2 libuuid1_2.35.2-2 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.35.2-2 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.2-1 perl-base_5.30.2-1 perl-modules-5.30_5.30.2-1 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seer-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.2-2 xz-utils_5.2.4-1 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 '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Jun 2 06:26:14 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./seer_1.1.4-3.dsc
dpkg-source: info: extracting seer in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking seer_1.1.4.orig.tar.gz
dpkg-source: info: unpacking seer_1.1.4-3.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
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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-1e93d5b9-87de-45b9-8fde-283e57c3fcf7
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 1.1.4-3
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
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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
g++ -g -O2 -fdebug-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++/9/vector:72,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sample>::iterator' {aka '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:71,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/ostream:38,
from /usr/include/c++/9/iostream:39,
from seercommon.hpp:10,
from seerIO.cpp:12:
/usr/include/c++/9/bits/predefined_ops.h: In member 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++/9/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
142 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/9/bits/predefined_ops.h:142:9: 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++/9/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/vector:72,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/9/bits/stl_vector.h: In static member function 'static bool arma::diskio::save_hdf5_binary(const arma::Mat<eT>&, const arma::hdf5_name&, std::string&) [with eT = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: 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
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/9/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++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: 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++/9/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
85 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
92 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/vector:67,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Kmer>::iterator' {aka '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/9/vector:72,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/c++/9/bits/stl_vector.h: In function 'void doLinear(Kmer&, const vec&, const mat&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-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++/9/vector:72,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
g++ -g -O2 -fdebug-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 -fdebug-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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<arma::Col<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<arma::Col<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/c++/9/bits/stl_vector.h: In function 'void newtonRaphson(Kmer&, const vec&, const mat&, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void doLogit(Kmer&, const vec&, const mat&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-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 -fdebug-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++/9/vector:72,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<DistanceElement>::iterator' {aka '__gnu_cxx::__normal_iterator<DistanceElement*, std::vector<DistanceElement> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/c++/9/bits/stl_vector.h: In function 'arma::mat dissimiliarityMatrix(const mat&, unsigned int)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DistanceElement*, std::vector<DistanceElement> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsMain.cpp:8:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<arma::Col<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<arma::Col<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >'} changed in GCC 7.1
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/9/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-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 -fdebug-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 -fdebug-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 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 -o seer
g++ -g -O2 -fdebug-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 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 -o kmds
g++ -g -O2 -fdebug-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 fasta.o significant_kmer.o mapMain.o mapCmdLine.o -lboost_program_options -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o map_back
g++ -g -O2 -fdebug-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 combineInit.o combineCmdLine.o combineKmers.o -lgzstream -lz -lboost_program_options -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o combineKmers
g++ -g -O2 -fdebug-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 significant_kmer.o filter_seer.o filterCmdLine.o -lboost_program_options -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o filter_seer
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
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_testroot -a
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 -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -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/kmds contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/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: package could avoid a useless dependency if debian/seer/usr/bin/seer debian/seer/usr/bin/kmds debian/seer/usr/bin/map_back debian/seer/usr/bin/combineKmers debian/seer/usr/bin/filter_seer 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_1.1.4-3_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.4-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../seer_1.1.4-3_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 2020-06-04T18:24:07Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.4-3_armhf.changes:
---------------------------
Format: 1.8
Date: Tue, 02 Jun 2020 03:35:16 +0530
Source: seer
Binary: seer seer-dbgsym
Architecture: armhf
Version: 1.1.4-3
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Pranav Ballaney <ballaneypranav@gmail.com>
Description:
seer - genomic sequence element (kmer) enrichment analysis
Changes:
seer (1.1.4-3) unstable; urgency=medium
.
* Team upload
.
[ Steffen Moeller ]
* d/u/metadata: yamllint
* Update metadata with ref to conda
.
[ Pranav Ballaney ]
* Add autopkgtests
* Add docs
.
[ Andreas Tille ]
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Secure URI in copyright format (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
* Fix permissions
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8921ee6c1fa9a745bab00d73d61715898a2ca74d 5740 seer_1.1.4-3_armhf.buildinfo
a327e6a70c54f8b7ca06216d5ea946881685433e 1067560 seer_1.1.4-3_armhf.deb
Checksums-Sha256:
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ac2f542b29991b7795d889b41a02fc9a10631b2fb9b54c4a88daf0bb9663d260 5740 seer_1.1.4-3_armhf.buildinfo
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Files:
288389284a57c41be0cc685aa3b3fdd0 8177316 debug optional seer-dbgsym_1.1.4-3_armhf.deb
0953c90dc748aab7cbf418f97401c901 5740 science optional seer_1.1.4-3_armhf.buildinfo
fc15e45c35ffdc5ce17c7db20b89e98c 1067560 science optional seer_1.1.4-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.4-3_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 8177316 bytes: control archive=804 bytes.
523 bytes, 12 lines control
614 bytes, 6 lines md5sums
Package: seer-dbgsym
Source: seer
Version: 1.1.4-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8541
Depends: seer (= 1.1.4-3)
Section: debug
Priority: optional
Description: debug symbols for seer
Build-Ids: 316cec61ca15a2da220c685807749aba9db1a96d 66c2c9c4959bf239b80c5553988cf2f7dc31e1ad 6cba028c04c1d970c277b8fae51fbe0c9f0b2276 6eac6cb477bc6ee03e76151f618ea1a6fe6a947d 9a4bb73fd1304181dcb7f0047cb17cb4467994b7
drwxr-xr-x root/root 0 2020-06-01 22:05 ./
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/debug/.build-id/31/
-rw-r--r-- root/root 523452 2020-06-01 22:05 ./usr/lib/debug/.build-id/31/6cec61ca15a2da220c685807749aba9db1a96d.debug
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/debug/.build-id/66/
-rw-r--r-- root/root 2667044 2020-06-01 22:05 ./usr/lib/debug/.build-id/66/c2c9c4959bf239b80c5553988cf2f7dc31e1ad.debug
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/debug/.build-id/6c/
-rw-r--r-- root/root 3180368 2020-06-01 22:05 ./usr/lib/debug/.build-id/6c/ba028c04c1d970c277b8fae51fbe0c9f0b2276.debug
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/debug/.build-id/6e/
-rw-r--r-- root/root 999104 2020-06-01 22:05 ./usr/lib/debug/.build-id/6e/ac6cb477bc6ee03e76151f618ea1a6fe6a947d.debug
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/debug/.build-id/9a/
-rw-r--r-- root/root 368024 2020-06-01 22:05 ./usr/lib/debug/.build-id/9a/4bb73fd1304181dcb7f0047cb17cb4467994b7.debug
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 988516 2020-06-01 22:05 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/seer.debug
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/share/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-06-01 22:05 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.4-3_armhf.deb
----------------------
new Debian package, version 2.0.
size 1067560 bytes: control archive=2652 bytes.
1399 bytes, 24 lines control
4248 bytes, 61 lines md5sums
Package: seer
Version: 1.1.4-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4460
Depends: libarmadillo9 (>= 1:9.800.4+dfsg), libblas3 | libblas.so.3, libboost-program-options1.67.0, libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgzstream0 (>= 1.5+dfsg), libhdf5-103-1, libstdc++6 (>= 9), 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 2020-06-01 22:05 ./
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/bin/
-rwxr-xr-x root/root 4597 2020-06-01 22:05 ./usr/bin/R_mds
-rwxr-xr-x root/root 3794 2020-06-01 22:05 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 2152 2020-06-01 22:05 ./usr/bin/blastn_to_phandango
-rwxr-xr-x root/root 104076 2020-06-01 22:05 ./usr/bin/combineKmers
-rwxr-xr-x root/root 71308 2020-06-01 22:05 ./usr/bin/filter_seer
-rwxr-xr-x root/root 1869 2020-06-01 22:05 ./usr/bin/hits_to_fastq
-rwxr-xr-x root/root 419980 2020-06-01 22:05 ./usr/bin/kmds
-rwxr-xr-x root/root 173708 2020-06-01 22:05 ./usr/bin/map_back
-rwxr-xr-x root/root 3200 2020-06-01 22:05 ./usr/bin/mapping_to_phandango
-rwxr-xr-x root/root 1208 2020-06-01 22:05 ./usr/bin/mash2matrix
-rwxr-xr-x root/root 2295 2020-06-01 22:05 ./usr/bin/reformat_output
-rwxr-xr-x root/root 567468 2020-06-01 22:05 ./usr/bin/seer
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/share/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/share/doc/seer/
-rw-r--r-- root/root 684 2020-06-01 22:05 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 328 2020-06-01 22:05 ./usr/share/doc/seer/README.source
-rw-r--r-- root/root 278 2020-06-01 22:05 ./usr/share/doc/seer/README.test
-rw-r--r-- root/root 928 2020-06-01 22:05 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1009 2020-06-01 22:05 ./usr/share/doc/seer/copyright
drwxr-xr-x root/root 0 2020-06-01 22:05 ./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 2020-06-01 22:05 ./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 2020-06-01 22:05 ./usr/share/doc/seer/examples/tests_passed
-rw-r--r-- root/root 1803 2020-06-01 22:05 ./usr/share/doc/seer/run-unit-test
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/share/man/
drwxr-xr-x root/root 0 2020-06-01 22:05 ./usr/share/man/man1/
-rw-r--r-- root/root 506 2020-06-01 22:05 ./usr/share/man/man1/R_mds.1.gz
-rw-r--r-- root/root 501 2020-06-01 22:05 ./usr/share/man/man1/blast_top_hits.1.gz
-rw-r--r-- root/root 461 2020-06-01 22:05 ./usr/share/man/man1/combineKmers.1.gz
-rw-r--r-- root/root 543 2020-06-01 22:05 ./usr/share/man/man1/filter_seer.1.gz
-rw-r--r-- root/root 408 2020-06-01 22:05 ./usr/share/man/man1/hits_to_fastq.1.gz
-rw-r--r-- root/root 906 2020-06-01 22:05 ./usr/share/man/man1/kmds.1.gz
-rw-r--r-- root/root 458 2020-06-01 22:05 ./usr/share/man/man1/map_back.1.gz
-rw-r--r-- root/root 432 2020-06-01 22:05 ./usr/share/man/man1/mapping_to_phandango.1.gz
-rw-r--r-- root/root 466 2020-06-01 22:05 ./usr/share/man/man1/mash2matrix.1.gz
-rw-r--r-- root/root 422 2020-06-01 22:05 ./usr/share/man/man1/reformat_output.1.gz
-rw-r--r-- root/root 995 2020-06-01 22:05 ./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: 110888
Build-Time: 839
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 497
Job: seer_1.1.4-3
Machine Architecture: armhf
Package: seer
Package-Time: 1387
Source-Version: 1.1.4-3
Space: 110888
Status: successful
Version: 1.1.4-3
--------------------------------------------------------------------------------
Finished at 2020-06-04T18:24:07Z
Build needed 00:23:07, 110888k disc space