seer →
1.1.4-1 →
armhf → 2017-10-03 05:30:53
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| seer 1.1.4-1 (armhf) Tue, 03 Oct 2017 05:22:23 +0000 |
+==============================================================================+
Package: seer
Version: 1.1.4-1
Source Version: 1.1.4-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-8cabae04-31d7-4662-b915-80d6a90668e8' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.1 MB]
Fetched 22.4 MB in 8s (2774 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://anonscm.debian.org/git/debian-med/seer.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/seer.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 981 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main seer 1.1.4-1 (dsc) [2033 B]
Get:2 http://172.17.0.1/private buster-staging/main seer 1.1.4-1 (tar) [972 kB]
Get:3 http://172.17.0.1/private buster-staging/main seer 1.1.4-1 (diff) [6896 B]
Fetched 981 kB in 0s (2148 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/seer-6AFrwX/seer-1.1.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-6AFrwX' 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-n0uKE9/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-n0uKE9/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-n0uKE9/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (7929 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libreadline5 libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 16 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15082 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 (>= 10), libarmadillo-dev (>= 1:6.700.6+dfsg-1~), libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev
Filtered Build-Depends: debhelper (>= 10), 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-n0uKE9/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-n0uKE9/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ Sources [549 B]
Get:5 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ Packages [629 B]
Fetched 2511 B in 0s (9283 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install seer build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libreadline5 libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-7 debhelper
dh-autoreconf dh-strip-nondeterminism file g++-7 gcc-7 gcc-7-base gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarmadillo-dev libarmadillo7 libarpack2 libarpack2-dev
libasan4 libatomic1 libblas-dev libblas3 libboost-dev
libboost-program-options-dev libboost-program-options1.62-dev
libboost-program-options1.62.0 libboost1.62-dev libbsd0 libcc1-0 libcilkrts5
libcroco3 libdlib-data libdlib-dev libdlib18
libfile-stripnondeterminism-perl libgcc-7-dev libgcc1 libgfortran4
libglib2.0-0 libgomp1 libgzstream-dev libgzstream0 libhdf5-100
libhdf5-cpp-100 libhdf5-dev libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libstdc++-7-dev libstdc++6 libsuperlu-dev
libsuperlu5 libsz2 libtimedate-perl libtool libubsan0 libxml2 m4 man-db
po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-7-locales dh-make gcc-7-doc libstdc++6-7-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan4-dbg liblsan0-dbg
libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg
gettext-doc libasprintf-dev libgettextpo-dev groff libitpp-dev liblapack-doc
libboost-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev libhdf5-doc libstdc++-7-doc
libsuperlu-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur 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 file gettext gettext-base groff-base
hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl
libarmadillo-dev libarmadillo7 libarpack2 libarpack2-dev libblas-dev
libblas3 libboost-dev libboost-program-options-dev
libboost-program-options1.62-dev libboost-program-options1.62.0
libboost1.62-dev libbsd0 libcroco3 libdlib-data libdlib-dev libdlib18
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgzstream-dev
libgzstream0 libhdf5-100 libhdf5-cpp-100 libhdf5-dev libicu57 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsuperlu-dev libsuperlu5 libsz2
libtimedate-perl libtool libxml2 m4 man-db po-debconf
sbuild-build-depends-seer-dummy zlib1g-dev
The following packages will be upgraded:
cpp-7 g++-7 gcc-7 gcc-7-base libasan4 libatomic1 libcc1-0 libcilkrts5
libgcc-7-dev libgcc1 libgomp1 libstdc++-7-dev libstdc++6 libubsan0
14 upgraded, 62 newly installed, 0 to remove and 2 not upgraded.
Need to get 119 MB of archives.
After this operation, 26.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-n0uKE9/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [840 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 7.2.0-7 [63.1 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf gcc-7-base armhf 7.2.0-7 [181 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:7.2.0-7 [38.7 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 7.2.0-7 [6728 B]
Get:6 http://172.17.0.1/private buster-staging/main armhf libasan4 armhf 7.2.0-7 [299 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libubsan0 armhf 7.2.0-7 [102 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libcilkrts5 armhf 7.2.0-7 [35.3 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf cpp-7 armhf 7.2.0-7 [5129 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 7.2.0-7 [30.2 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-7 armhf 7.2.0-7 [5576 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf gcc-7 armhf 7.2.0-7 [5450 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-7-dev armhf 7.2.0-7 [666 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libstdc++-7-dev armhf 7.2.0-7 [1498 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 7.2.0-7 [335 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-2 [95.8 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-4 [609 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.0-1 [2650 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.8 [973 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-4 [36.0 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libaec0 armhf 0.3.2-2 [19.3 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.2.0-7 [188 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.7.1-4 [103 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.7.1-4 [1508 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libarpack2 armhf 3.5.0+real-1 [80.2 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libsuperlu5 armhf 5.2.1+dfsg1-2 [126 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libarmadillo7 armhf 1:7.960.1+dfsg-1 [79.7 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-4 [112 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.7.1-4 [1564 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libarpack2-dev armhf 3.5.0+real-1 [86.6 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libsz2 armhf 0.3.2-2 [6080 B]
Get:57 http://172.17.0.1/private buster-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-4 [1220 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2 [110 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2 [178 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 0.3.2-2 [17.3 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-4 [118 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-4 [2109 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-2 [18.0 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libarmadillo-dev armhf 1:7.960.1+dfsg-1 [329 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b6 [3916 B]
Get:69 http://172.17.0.1/private buster-staging/main armhf libboost-program-options1.62.0 armhf 1.62.0+dfsg-4 [136 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libboost-program-options1.62-dev armhf 1.62.0+dfsg-4 [178 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libboost-program-options-dev armhf 1.62.0.1+b6 [3712 B]
Get:72 http://172.17.0.1/private buster-staging/main armhf libdlib-data all 18.18-2 [63.4 MB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libdlib18 armhf 18.18-2 [223 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libdlib-dev armhf 18.18-2 [1356 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libgzstream0 armhf 1.5+dfsg-2 [5764 B]
Get:76 http://172.17.0.1/private buster-staging/main armhf libgzstream-dev armhf 1.5+dfsg-2 [6172 B]
debconf: delaying package configuration, since apt-utils is not installed
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-3+rpi1 dpkg-dev_1.18.24 g++-7_7.2.0-7 gcc-7_7.2.0-7 libc6-dev_2.24-14 libstdc++-7-dev_7.2.0-7 libstdc++6_7.2.0-7 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch
Package versions: adduser_3.116 apt_1.5 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-3+rpi1 binutils-arm-linux-gnueabihf_2.29.1-3+rpi1 binutils-common_2.29.1-3+rpi1 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-7 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.8 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dirmngr_2.2.1-1 dmsetup_2:1.02.142-1 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.6-1 e2fsprogs_1.43.6-1 fakeroot_1.22-1 fdisk_2.29.2-5 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-7 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-7 gcc-7-base_7.2.0-7 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-1 gnupg-agent_2.2.1-1 gnupg-l10n_2.2.1-1 gnupg-utils_2.2.1-1 gpg_2.2.1-1 gpg-agent_2.2.1-1 gpg-wks-client_2.2.1-1 gpg-wks-server_2.2.1-1 gpgconf_2.2.1-1 gpgsm_2.2.1-1 gpgv_2.2.1-1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-4 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libaec-dev_0.3.2-2 libaec0_0.3.2-2 libapparmor1_2.11.0-11 libapt-pkg5.0_1.5 libarchive-zip-perl_1.59-1 libarmadillo-dev_1:7.960.1+dfsg-1 libarmadillo7_1:7.960.1+dfsg-1 libarpack2_3.5.0+real-1 libarpack2-dev_3.5.0+real-1 libasan4_7.2.0-7 libassuan0_2.4.3-3 libatomic1_7.2.0-7 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libbinutils_2.29.1-3+rpi1 libblas-dev_3.7.1-4 libblas3_3.7.1-4 libblkid1_2.29.2-5 libboost-dev_1.62.0.1+b6 libboost-program-options-dev_1.62.0.1+b6 libboost-program-options1.62-dev_1.62.0+dfsg-4 libboost-program-options1.62.0_1.62.0+dfsg-4 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.6-2 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-14 libc-dev-bin_2.24-14 libc6_2.24-14 libc6-dev_2.24-14 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.2.0-7 libcilkrts5_7.2.0-7 libcomerr2_1.43.6-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.16+really1.10.22-1 libdebconfclient0_0.230 libdevmapper1.02.1_2:1.02.142-1 libdlib-data_18.18-2 libdlib-dev_18.18-2 libdlib18_18.18-2 libdpkg-perl_1.18.24 libdrm-common_2.4.82-1+rpi1 libdrm2_2.4.82-1+rpi1 libfakeroot_1.22-1 libfdisk1_2.29.2-5 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-7-dev_7.2.0-7 libgcc1_1:7.2.0-7 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libgfortran4_7.2.0-7 libglib2.0-0_2.54.0-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.15-2 libgomp1_7.2.0-7 libgpg-error0_1.27-3 libgzstream-dev_1.5+dfsg-2 libgzstream0_1.5+dfsg-2 libhdf5-100_1.10.0-patch1+docs-4 libhdf5-cpp-100_1.10.0-patch1+docs-4 libhdf5-dev_1.10.0-patch1+docs-4 libhogweed4_3.3-2 libicu57_57.1-6 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2 libisl15_0.18-1 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2 libjpeg62-turbo-dev_1:1.5.2-2 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 liblapack-dev_3.7.1-4 liblapack3_3.7.1-4 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.29.2-5 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.0-8 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.32-3 libprocps6_2:3.3.12-3 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.29.2-5 libsqlite3-0_3.20.1-1 libss2_1.43.6-1 libssl1.1_1.1.0f-5 libstdc++-7-dev_7.2.0-7 libstdc++6_7.2.0-7 libsuperlu-dev_5.2.1+dfsg1-2 libsuperlu5_5.2.1+dfsg1-2 libsystemd0_234-3 libsz2_0.3.2-2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-7 libudev1_234-3 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-5 libxml2_2.9.4+dfsg1-4 linux-base_4.5 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch login_1:4.4-4.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-5 mountall_2.54 multiarch-support_2.24-14 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0f-5 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-8 perl-base_5.26.0-8 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-8 pinentry-curses_1.0.0-2 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seer-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017b-2 udev_234-3 util-linux_2.29.2-5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Sep 28 14:04:26 2017 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_1.1.4-1.dsc
dpkg-source: info: extracting seer in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking seer_1.1.4.orig.tar.gz
dpkg-source: info: unpacking seer_1.1.4-1.debian.tar.xz
dpkg-source: info: applying fix_lib_location.patch
dpkg-source: info: applying hardening.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-8cabae04-31d7-4662-b915-80d6a90668e8
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package seer
dpkg-buildpackage: info: source version 1.1.4-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build seer-1.1.4
dpkg-buildpackage: info: host architecture armhf
fakeroot 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_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4
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 between signed and unsigned integer expressions [-Wsign-compare]
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++/7/vector:69:0,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:71:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/ios:40,
from /usr/include/c++/7/ostream:38,
from /usr/include/c++/7/iostream:39,
from seercommon.hpp:10,
from seerIO.cpp:12:
/usr/include/c++/7/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++/7/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
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/7/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++/7/algorithm:62:0,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/7/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++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1847:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
if (__comp(__i, __first))
~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/7/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++/7/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
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/7/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++/7/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:222:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
if (__comp(__first + __secondChild,
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
__first + (__secondChild - 1)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/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
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/7/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++/7/algorithm:62:0,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/7/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++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:81:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
if (__comp(__a, __b))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/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
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/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
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/7/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++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:394:7: 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
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
_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++/7/vector:69:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In function 'void doLinear(Kmer&, const vec&, const mat&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In function 'void newtonRaphson(Kmer&, const vec&, const mat&, bool)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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
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
/usr/include/c++/7/bits/stl_vector.h: In function 'void doLogit(Kmer&, const vec&, const mat&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 kmdsCmdLine.o kmdsCmdLine.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 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++/7/vector:69:0,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:394:7: 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
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In function 'arma::mat dissimiliarityMatrix(const mat&, unsigned int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DistanceElement*, std::vector<DistanceElement> >' changed in GCC 7.1
_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 mapCmdLine.o mapCmdLine.cpp
In file included from /usr/include/c++/7/vector:69:0,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsMain.cpp:8:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
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
/usr/include/c++/7/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
_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 combineKmers.o combineKmers.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 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
fakeroot debian/rules binary-arch
dh binary-arch
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 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
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/seer/usr/bin/kmds contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/filter_seer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/combineKmers contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/map_back contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/seer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/kmds debian/seer/usr/bin/filter_seer debian/seer/usr/bin/combineKmers debian/seer/usr/bin/map_back debian/seer/usr/bin/seer were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/kmds debian/seer/usr/bin/combineKmers debian/seer/usr/bin/seer were not linked against libz.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/kmds debian/seer/usr/bin/seer were not linked against liblapack.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_1.1.4-1_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.4-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../seer_1.1.4-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build seer-1.1.4
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-10-03T05:30:50Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.4-1_armhf.changes:
---------------------------
Format: 1.8
Date: Thu, 28 Sep 2017 13:20:25 +0200
Source: seer
Binary: seer
Architecture: armhf
Version: 1.1.4-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
seer - genomic sequence element (kmer) enrichment analysis
Changes:
seer (1.1.4-1) unstable; urgency=medium
.
* New upstream version
* Standards-Version: 4.1.0 (no changes needed)
Checksums-Sha1:
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e600a3bc60f31adc1858462c503c7a6559e9b8f0 5385 seer_1.1.4-1_armhf.buildinfo
f629d7106599cad5e027d807dfb3d0e61022a7ea 297588 seer_1.1.4-1_armhf.deb
Checksums-Sha256:
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6f978d34b6ad5d13acfc72288e5718cfbb46bf390e4d9ecbc2aa4d69a02f063b 5385 seer_1.1.4-1_armhf.buildinfo
7ef85c4ea4fec1a94cb9b3c6505fb3d217a0485114af81c6a335084a28a3cef2 297588 seer_1.1.4-1_armhf.deb
Files:
03470ef3176a89bb046dbfafac089655 7170428 debug optional seer-dbgsym_1.1.4-1_armhf.deb
c06a9bcda38c3add2b9fc5f120361010 5385 science optional seer_1.1.4-1_armhf.buildinfo
15df9536152e7fe5b3332709e4f059b2 297588 science optional seer_1.1.4-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.4-1_armhf.deb
-----------------------------
new debian package, version 2.0.
size 7170428 bytes: control archive=679 bytes.
523 bytes, 12 lines control
530 bytes, 5 lines md5sums
Package: seer-dbgsym
Source: seer
Version: 1.1.4-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7533
Depends: seer (= 1.1.4-1)
Section: debug
Priority: optional
Description: debug symbols for seer
Build-Ids: 30bf73c4b0df70a27af41f51a63018cf8492134d 61d7fc74346f540d65429822e4bc7ec7c00ab69d a8fc434da3c0af5e7a218b37dc2415c04a1735eb c99cfd4384f924c3178ca70855de67f43cab60c6 d0b9852e4a5d84d328e589497feb812da7e045eb
drwxr-xr-x root/root 0 2017-09-28 11:20 ./
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/30/
-rw-r--r-- root/root 3317672 2017-09-28 11:20 ./usr/lib/debug/.build-id/30/bf73c4b0df70a27af41f51a63018cf8492134d.debug
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/61/
-rw-r--r-- root/root 350480 2017-09-28 11:20 ./usr/lib/debug/.build-id/61/d7fc74346f540d65429822e4bc7ec7c00ab69d.debug
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/a8/
-rw-r--r-- root/root 2752056 2017-09-28 11:20 ./usr/lib/debug/.build-id/a8/fc434da3c0af5e7a218b37dc2415c04a1735eb.debug
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/c9/
-rw-r--r-- root/root 795512 2017-09-28 11:20 ./usr/lib/debug/.build-id/c9/9cfd4384f924c3178ca70855de67f43cab60c6.debug
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/d0/
-rw-r--r-- root/root 481288 2017-09-28 11:20 ./usr/lib/debug/.build-id/d0/b9852e4a5d84d328e589497feb812da7e045eb.debug
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-09-28 11:20 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.4-1_armhf.deb
----------------------
new debian package, version 2.0.
size 297588 bytes: control archive=1812 bytes.
1412 bytes, 24 lines control
1705 bytes, 27 lines md5sums
Package: seer
Version: 1.1.4-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1262
Depends: libarmadillo7, libblas3 | libblas.so.3, libboost-program-options1.62.0, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgzstream0, libhdf5-100, liblapack3 | liblapack.so.3, 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 2017-09-28 11:20 ./
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/bin/
-rwxr-xr-x root/root 4597 2017-09-28 11:20 ./usr/bin/R_mds
-rwxr-xr-x root/root 3794 2017-09-28 11:20 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 2152 2017-09-28 11:20 ./usr/bin/blastn_to_phandango
-rwxr-xr-x root/root 103944 2017-09-28 11:20 ./usr/bin/combineKmers
-rwxr-xr-x root/root 71176 2017-09-28 11:20 ./usr/bin/filter_seer
-rwxr-xr-x root/root 1869 2017-09-28 11:20 ./usr/bin/hits_to_fastq
-rwxr-xr-x root/root 374792 2017-09-28 11:20 ./usr/bin/kmds
-rwxr-xr-x root/root 177672 2017-09-28 11:20 ./usr/bin/map_back
-rwxr-xr-x root/root 3200 2017-09-28 11:20 ./usr/bin/mapping_to_phandango
-rwxr-xr-x root/root 1208 2017-09-28 11:20 ./usr/bin/mash2matrix
-rwxr-xr-x root/root 2295 2017-09-28 11:20 ./usr/bin/reformat_output
-rwxr-xr-x root/root 509992 2017-09-28 11:20 ./usr/bin/seer
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/doc/seer/
-rw-r--r-- root/root 684 2017-09-28 11:20 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 537 2017-09-28 11:20 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1008 2017-09-28 11:20 ./usr/share/doc/seer/copyright
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/doc/seer/examples/
-rw-r--r-- root/root 2110 2017-06-20 09:43 ./usr/share/doc/seer/examples/example_wrapper.py.gz
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/man/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/man/man1/
-rw-r--r-- root/root 506 2017-09-28 11:20 ./usr/share/man/man1/R_mds.1.gz
-rw-r--r-- root/root 501 2017-09-28 11:20 ./usr/share/man/man1/blast_top_hits.1.gz
-rw-r--r-- root/root 461 2017-09-28 11:20 ./usr/share/man/man1/combineKmers.1.gz
-rw-r--r-- root/root 543 2017-09-28 11:20 ./usr/share/man/man1/filter_seer.1.gz
-rw-r--r-- root/root 408 2017-09-28 11:20 ./usr/share/man/man1/hits_to_fastq.1.gz
-rw-r--r-- root/root 906 2017-09-28 11:20 ./usr/share/man/man1/kmds.1.gz
-rw-r--r-- root/root 458 2017-09-28 11:20 ./usr/share/man/man1/map_back.1.gz
-rw-r--r-- root/root 432 2017-09-28 11:20 ./usr/share/man/man1/mapping_to_phandango.1.gz
-rw-r--r-- root/root 466 2017-09-28 11:20 ./usr/share/man/man1/mash2matrix.1.gz
-rw-r--r-- root/root 422 2017-09-28 11:20 ./usr/share/man/man1/reformat_output.1.gz
-rw-r--r-- root/root 995 2017-09-28 11:20 ./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: 76128
Build-Time: 263
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 229
Job: seer_1.1.4-1
Machine Architecture: armhf
Package: seer
Package-Time: 507
Source-Version: 1.1.4-1
Space: 76128
Status: successful
Version: 1.1.4-1
--------------------------------------------------------------------------------
Finished at 2017-10-03T05:30:50Z
Build needed 00:08:27, 76128k disk space