snp-sites →
2.5.1-2 →
armhf → 2021-10-05 06:42:36
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| snp-sites 2.5.1-2 (armhf) Tue, 05 Oct 2021 06:31:54 +0000 |
+==============================================================================+
Package: snp-sites
Version: 2.5.1-2
Source Version: 2.5.1-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-0c95c0ed-35a9-4c88-ba27-49e3b5c38e0e' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 27s (956 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: 'snp-sites' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/snp-sites.git
Please use:
git clone https://salsa.debian.org/med-team/snp-sites.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 15.6 MB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main snp-sites 2.5.1-2 (dsc) [2297 B]
Get:2 http://172.17.0.1/private bookworm-staging/main snp-sites 2.5.1-2 (tar) [15.6 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main snp-sites 2.5.1-2 (diff) [8252 B]
Fetched 15.6 MB in 1s (11.7 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/snp-sites-hns9pj/snp-sites-2.5.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/snp-sites-hns9pj' 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-dKmxhu/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-dKmxhu/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-dKmxhu/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-dKmxhu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2660 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 22 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, check, pkg-config, d-shlibs, asciidoctor
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, check, pkg-config, d-shlibs, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-snp-sites-dummy' in '/<<BUILDDIR>>/resolver-dKmxhu/apt_archive/sbuild-build-depends-snp-sites-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-snp-sites-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-dKmxhu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ Sources [529 B]
Get:5 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ Packages [610 B]
Fetched 2472 B in 1s (3174 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install snp-sites 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:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates check d-shlibs debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libdebhelper-perl libedit2
libelf1 libffi8 libfile-stripnondeterminism-perl libglib2.0-0 libicu67
libmagic-mgc libmagic1 libmd0 libpipeline1 libruby2.7 libsigsegv2
libsub-override-perl libsubunit-dev libsubunit0 libtool libuchardet0 libxml2
libyaml-0-2 m4 man-db openssl pkg-config po-debconf rake ruby
ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert
ruby-rubygems ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration
sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl ri ruby-dev bundler
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates check d-shlibs debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libdebhelper-perl libedit2
libelf1 libffi8 libfile-stripnondeterminism-perl libglib2.0-0 libicu67
libmagic-mgc libmagic1 libmd0 libpipeline1 libruby2.7 libsigsegv2
libsub-override-perl libsubunit-dev libsubunit0 libtool libuchardet0 libxml2
libyaml-0-2 m4 man-db openssl pkg-config po-debconf rake ruby
ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert
ruby-rubygems ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration
sbuild-build-depends-snp-sites-dummy sensible-utils zlib1g-dev
0 upgraded, 59 newly installed, 0 to remove and 22 not upgraded.
Need to get 25.9 MB of archives.
After this operation, 92.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-dKmxhu/apt_archive ./ sbuild-build-depends-snp-sites-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf openssl armhf 1.1.1l-1 [815 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf ca-certificates all 20210119 [158 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf rubygems-integration all 1.18 [6704 B]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf rake all 13.0.3-1 [84.7 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf ruby-minitest all 5.13.0-1 [57.3 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf ruby-power-assert all 1.1.7-2 [11.5 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf ruby-test-unit all 3.3.9-1 [86.1 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.3-3 [27.2 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-2 [21.2 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libyaml-0-2 armhf 0.2.2-1 [40.0 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libruby2.7 armhf 2.7.4-1+b1 [3902 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf ruby2.7 armhf 2.7.4-1+b1 [747 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf ruby-rubygems all 3.2.27-1 [272 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf ruby armhf 1:2.7+2 [11.7 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf ruby-asciidoctor all 2.0.16-1 [210 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf asciidoctor all 2.0.16-1 [87.5 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libsubunit0 armhf 1.4.0-3 [9536 B]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libsubunit-dev armhf 1.4.0-3 [10.5 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf check armhf 0.15.2-2 [116 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf d-shlibs all 0.100 [18.1 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.0-1 [1208 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libdebhelper-perl (13.5.2) ...
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Unpacking dh-autoreconf (20) ...
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Unpacking libsub-override-perl (0.09-2) ...
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Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ...
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Unpacking dh-strip-nondeterminism (1.12.0-1) ...
Selecting previously unselected package libelf1:armhf.
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Unpacking libelf1:armhf (0.185-2) ...
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Unpacking dwz (0.14-1) ...
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Unpacking libicu67:armhf (67.1-7) ...
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Unpacking libxml2:armhf (2.9.12+dfsg-5) ...
Selecting previously unselected package gettext.
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Unpacking gettext (0.21-4) ...
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Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
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Unpacking po-debconf (1.0.21+nmu1) ...
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Unpacking debhelper (13.5.2) ...
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Unpacking libglib2.0-0:armhf (2.70.0-1) ...
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Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-snp-sites-dummy.
Preparing to unpack .../58-sbuild-build-depends-snp-sites-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-snp-sites-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up bsdextrautils (2.37.2-1) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up ruby-power-assert (1.1.7-2) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:armhf (0.2.2-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libsubunit0:armhf (1.4.0-3) ...
Setting up ruby-minitest (5.13.0-1) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up ruby-test-unit (3.3.9-1) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up d-shlibs (0.100) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libffi8:armhf (3.4.2-2) ...
Setting up libmd0:armhf (1.0.3-3) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up openssl (1.1.1l-1) ...
Setting up libbsd0:armhf (0.11.3-1) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up ruby-xmlrpc (0.3.0-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up libglib2.0-0:armhf (2.70.0-1) ...
No schema files found: doing nothing.
Setting up libedit2:armhf (3.1-20210910-1) ...
Setting up libsubunit-dev:armhf (1.4.0-3) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
129 added, 0 removed; done.
Setting up check:armhf (0.15.2-2) ...
Setting up pkg-config (0.29.2-1) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up rubygems-integration (1.18) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up ruby2.7 (2.7.4-1+b1) ...
Setting up ruby-rubygems (3.2.27-1) ...
Setting up ruby (1:2.7+2) ...
Setting up ruby-asciidoctor (2.0.16-1) ...
Setting up rake (13.0.3-1) ...
Setting up asciidoctor (2.0.16-1) ...
Setting up sbuild-build-depends-snp-sites-dummy (0.invalid.0) ...
Setting up libruby2.7:armhf (2.7.4-1+b1) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
Processing triggers for ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
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_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 asciidoctor_2.0.16-1 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 ca-certificates_20210119 check_0.15.2-2 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 d-shlibs_0.100 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libedit2_3.1-20210910-1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-2 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libglib2.0-0_2.70.0-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.3-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libreadline8_8.1-2 libruby2.7_2.7.4-1+b1 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsubunit-dev_1.4.0-3 libsubunit0_1.4.0-3 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libyaml-0-2_0.2.2-1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 openssl_1.1.1l-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 rake_13.0.3-1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 ruby_1:2.7+2 ruby-asciidoctor_2.0.16-1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-2 ruby-rubygems_3.2.27-1 ruby-test-unit_3.3.9-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.4-1+b1 rubygems-integration_1.18 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-snp-sites-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.PC1CCN53/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct 1 14:19:48 2021 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 ./snp-sites_2.5.1-2.dsc
dpkg-source: info: extracting snp-sites in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking snp-sites_2.5.1.orig.tar.gz
dpkg-source: info: unpacking snp-sites_2.5.1-2.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-0c95c0ed-35a9-4c88-ba27-49e3b5c38e0e
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package snp-sites
dpkg-buildpackage: info: source version 2.5.1-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:16: warning: The macro `AC_LANG_C' is obsolete.
configure.ac:16: You should run autoupdate.
./lib/autoconf/c.m4:72: AC_LANG_C is expanded from...
m4/m4_ax_check_zlib.m4:68: AX_CHECK_ZLIB is expanded from...
configure.ac:16: the top level
configure.ac:18: warning: The macro `AC_PROG_LIBTOOL' is obsolete.
configure.ac:18: You should run autoupdate.
m4/libtool.m4:99: AC_PROG_LIBTOOL is expanded from...
configure.ac:18: the top level
configure.ac:14: installing './compile'
configure.ac:7: installing './config.guess'
configure.ac:7: installing './config.sub'
configure.ac:2: installing './install-sh'
configure.ac:2: installing './missing'
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for check >= 0.8.2... yes
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for zlib.h... yes
checking for math.h... yes
checking for getopt.h... yes
checking for floor in -lm... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking for zlib.h... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
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/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylib-of-snp-sites.lo phylib-of-snp-sites.c
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c phylib-of-snp-sites.c -fPIC -DPIC -o .libs/phylib-of-snp-sites.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp-sites.lo snp-sites.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c phylib-of-snp-sites.c -o phylib-of-snp-sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fasta-of-snp-sites.lo fasta-of-snp-sites.c
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libtool: link: gcc --std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/snp-sites snp_sites-main.o -L/usr/lib ./.libs/libsnp-sites.so -lpthread -lz -lm
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gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check-snp-sites.o `test -f '../tests/check-snp-sites.c' || echo './'`../tests/check-snp-sites.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check-vcf.o `test -f '../tests/check-vcf.c' || echo './'`../tests/check-vcf.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper-methods.o `test -f '../tests/helper-methods.c' || echo './'`../tests/helper-methods.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run-all-tests.o `test -f '../tests/run-all-tests.c' || echo './'`../tests/run-all-tests.c
In file included from ../tests/check-snp-sites.c:23:
../tests/check-snp-sites.c: In function 'valid_alignment_with_one_line_per_sequence_fn':
../tests/check-snp-sites.c:40:147: warning: too many arguments for format [-Wformat-extra-args]
40 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:41:153: warning: too many arguments for format [-Wformat-extra-args]
41 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:42:167: warning: too many arguments for format [-Wformat-extra-args]
42 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_alignment_with_n_as_gap_fn':
../tests/check-snp-sites.c:53:118: warning: too many arguments for format [-Wformat-extra-args]
53 | fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.vcf", "alignment_file_with_n.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:54:124: warning: too many arguments for format [-Wformat-extra-args]
54 | fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.phylip", "alignment_file_with_n.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:55:138: warning: too many arguments for format [-Wformat-extra-args]
55 | fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.snp_sites.aln","alignment_file_with_n.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_alignment_with_one_line_per_sequence_gzipped_fn':
../tests/check-snp-sites.c:67:150: warning: too many arguments for format [-Wformat-extra-args]
67 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.gz.vcf" ) == 1, "Invalid VCF file for 1 line per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:68:156: warning: too many arguments for format [-Wformat-extra-args]
68 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.gz.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:69:170: warning: too many arguments for format [-Wformat-extra-args]
69 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.gz.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_alignment_with_multiple_lines_per_sequence_fn':
../tests/check-snp-sites.c:79:155: warning: too many arguments for format [-Wformat-extra-args]
79 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_multiple_lines_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:80:161: warning: too many arguments for format [-Wformat-extra-args]
80 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_multiple_lines_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:81:174: warning: too many arguments for format [-Wformat-extra-args]
81 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_alignment_with_pure_mode_fn':
../tests/check-snp-sites.c:91:115: warning: too many arguments for format [-Wformat-extra-args]
91 | fail_unless( compare_files("../tests/data/pure_mode_alignment.aln.vcf", "pure_mode_alignment.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:92:121: warning: too many arguments for format [-Wformat-extra-args]
92 | fail_unless( compare_files("../tests/data/pure_mode_alignment.aln.phylip", "pure_mode_alignment.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:93:134: warning: too many arguments for format [-Wformat-extra-args]
93 | fail_unless( compare_files("../tests/data/pure_mode_alignment.aln.snp_sites.aln","pure_mode_alignment.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_alignment_with_monomorphic_sites_fn':
../tests/check-snp-sites.c:103:139: warning: too many arguments for format [-Wformat-extra-args]
103 | fail_unless( compare_files("../tests/data/pure_mode_monomorphic_alignment.aln.vcf", "pure_mode_monomorphic_alignment.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:104:145: warning: too many arguments for format [-Wformat-extra-args]
104 | fail_unless( compare_files("../tests/data/pure_mode_monomorphic_alignment.aln.phylip", "pure_mode_monomorphic_alignment.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:105:158: warning: too many arguments for format [-Wformat-extra-args]
105 | fail_unless( compare_files("../tests/data/pure_mode_monomorphic_alignment.aln.snp_sites.aln","pure_mode_monomorphic_alignment.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_with_only_aln_file_output_default_fn':
../tests/check-snp-sites.c:116:169: warning: too many arguments for format [-Wformat-extra-args]
116 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_with_only_aln_file_output_fn':
../tests/check-snp-sites.c:124:169: warning: too many arguments for format [-Wformat-extra-args]
124 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_with_only_aln_file_output_with_custom_name_fn':
../tests/check-snp-sites.c:133:131: warning: too many arguments for format [-Wformat-extra-args]
133 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","some_custom_name" ) == 1 ,"Only aln with custom name should be outputted");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_with_phylip_outputted_with_custom_name_fn':
../tests/check-snp-sites.c:141:122: warning: too many arguments for format [-Wformat-extra-args]
141 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "some_custom_name" ) == 1, "Custom name needs extra extension for phylip" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_with_all_outputted_with_custom_name_fn':
../tests/check-snp-sites.c:157:123: warning: too many arguments for format [-Wformat-extra-args]
157 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "some_custom_name.vcf" ) == 1, "Custom name needs extra extension for VCF" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:158:129: warning: too many arguments for format [-Wformat-extra-args]
158 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "some_custom_name.phylip" ) == 1, "Custom name needs extra extension for phylip" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c:159:143: warning: too many arguments for format [-Wformat-extra-args]
159 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","some_custom_name.snp_sites.aln" ) == 1 , "Custom name needs extra extension for ALN");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_aln_plus_reference_fn':
../tests/check-snp-sites.c:170:175: warning: too many arguments for format [-Wformat-extra-args]
170 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence_reference.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check-snp-sites.c: In function 'valid_phylip_plus_reference_fn':
../tests/check-snp-sites.c:178:163: warning: too many arguments for format [-Wformat-extra-args]
178 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence_reference.aln.phylip", "alignment_file_one_line_per_sequence.aln.phylip" ) == 1, "invalid phylib with reference" );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CC --mode=link gcc -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o run-all-tests ../tests/run_all_tests-check-snp-sites.o ../tests/run_all_tests-check-vcf.o ../tests/run_all_tests-helper-methods.o ../tests/run_all_tests-run-all-tests.o libsnp-sites.la -lpthread -lcheck_pic -pthread -lrt -lm -lsubunit -lz -lm
libtool: link: gcc -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run-all-tests ../tests/run_all_tests-check-snp-sites.o ../tests/run_all_tests-check-vcf.o ../tests/run_all_tests-helper-methods.o ../tests/run_all_tests-run-all-tests.o -pthread -L/usr/lib ./.libs/libsnp-sites.so -lpthread -lcheck_pic -lrt -lsubunit -lz -lm -pthread
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PASS: run-all-tests
============================================================================
Testsuite summary for snp-sites 2.5.1
============================================================================
# TOTAL: 1
# PASS: 1
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
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make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c libsnp-sites.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libsnp-sites.so.1.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libsnp-sites.so.1.0.0 libsnp-sites.so.1 || { rm -f libsnp-sites.so.1 && ln -s libsnp-sites.so.1.0.0 libsnp-sites.so.1; }; })
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libsnp-sites.so.1.0.0 libsnp-sites.so || { rm -f libsnp-sites.so && ln -s libsnp-sites.so.1.0.0 libsnp-sites.so; }; })
libtool: install: /usr/bin/install -c .libs/libsnp-sites.lai /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.la
libtool: install: /usr/bin/install -c .libs/libsnp-sites.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c snp-sites '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
libtool: warning: 'libsnp-sites.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/snp-sites /<<PKGBUILDDIR>>/debian/tmp/usr/bin/snp-sites
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/snp-sites'
/usr/bin/install -c -m 644 alignment-file.h vcf.h phylib-of-snp-sites.h snp-sites.h fasta-of-snp-sites.h kseq.h '/<<PKGBUILDDIR>>/debian/tmp/usr/include/snp-sites'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
d-shlibmove --commit \
--multiarch \
--exclude-la \
--movedev "debian/tmp/usr/include/snp-sites/*.h" usr/include/snp-sites \
debian/tmp/usr/lib/*/libsnp-sites.so
Library package automatic movement utility
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1 debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0 debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf
PKGDEV=libsnp-sites1-dev
PKGSHL=libsnp-sites1
install -d -m 755 debian/libsnp-sites1-dev/usr/include/snp-sites
mv debian/tmp/usr/include/snp-sites/*.h debian/libsnp-sites1-dev/usr/include/snp-sites
find debian -name "lib*.la" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/debian/man
asciidoctor -a docdate='' -b manpage /<<PKGBUILDDIR>>/snp-sites.txt
mv /<<PKGBUILDDIR>>/snp-sites.1 /<<PKGBUILDDIR>>/debian/man
dh_installman --
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/snp-sites/usr/bin/snp-sites was not linked against libpthread.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/snp-sites/usr/bin/snp-sites was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package libsnp-sites1-dev: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: package libsnp-sites1-dev: substitution variable ${devlibs:Depends} unused, but is defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'snp-sites' in '../snp-sites_2.5.1-2_armhf.deb'.
dpkg-deb: building package 'libsnp-sites1' in '../libsnp-sites1_2.5.1-2_armhf.deb'.
dpkg-deb: building package 'libsnp-sites1-dev' in '../libsnp-sites1-dev_2.5.1-2_armhf.deb'.
dpkg-deb: building package 'snp-sites-dbgsym' in '../snp-sites-dbgsym_2.5.1-2_armhf.deb'.
dpkg-deb: building package 'libsnp-sites1-dbgsym' in '../libsnp-sites1-dbgsym_2.5.1-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../snp-sites_2.5.1-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-10-05T06:42:29Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
snp-sites_2.5.1-2_armhf.changes:
--------------------------------
Format: 1.8
Date: Fri, 01 Oct 2021 16:16:44 +0200
Source: snp-sites
Binary: libsnp-sites1 libsnp-sites1-dbgsym libsnp-sites1-dev snp-sites snp-sites-dbgsym
Architecture: armhf
Version: 2.5.1-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
libsnp-sites1 - Shared libraries of the package snp-sites
libsnp-sites1-dev - Static libraries and header files for the package snp-sites
snp-sites - Binary code for the package snp-sites
Changes:
snp-sites (2.5.1-2) unstable; urgency=medium
.
* Fix watch file
* Standards-Version: 4.6.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Remove trailing whitespace in debian/changelog (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* No tab in license text (routine-update)
* Trim trailing whitespace.
* Set upstream metadata fields: Bug-Database, Bug-Submit.
* Apply multi-arch hints.
+ libsnp-sites1, libsnp-sites1-dev: Add Multi-Arch: same.
* Remove *.la file which should not be installed
Checksums-Sha1:
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3448afc994d27ed09b21fd4dfc01aaf24807a938 16520 libsnp-sites1-dev_2.5.1-2_armhf.deb
f999d5b6d526562185553134f6b2bb6a9169573e 13340 libsnp-sites1_2.5.1-2_armhf.deb
4417bd6c9a7a57e5abb1d1e3c9f94724334280c0 6496 snp-sites-dbgsym_2.5.1-2_armhf.deb
f9ae14747cab330b3cdf238e58e364bcdd2ace79 7430 snp-sites_2.5.1-2_armhf.buildinfo
ed6322baf3e47cdf1a4f7882323c9369a3e844bd 14116 snp-sites_2.5.1-2_armhf.deb
Checksums-Sha256:
71a3b0fa3b4a65b4e9eca9e792ea63f9e3fbb642e846766c89460a11378faac5 20164 libsnp-sites1-dbgsym_2.5.1-2_armhf.deb
f8f2108564efb30affac228a1d40b5863be5966b00e5c051b0dccefb0fde1440 16520 libsnp-sites1-dev_2.5.1-2_armhf.deb
70af547d7bd9c24c056ddb730aaae00cf152bd6de0ad1907616d48571bb2abf2 13340 libsnp-sites1_2.5.1-2_armhf.deb
356717d343fbe1a576688ce8938732ad0ef8a7af92d671108a130353129e15d0 6496 snp-sites-dbgsym_2.5.1-2_armhf.deb
5f29a7f4e9d9bc8648c2cbc0e08b61c30453556df24c576bab40884f967d2ba2 7430 snp-sites_2.5.1-2_armhf.buildinfo
bd6f2c08567dae3fe4a03e83ae3dbe627e16b3b0243c8e9ecd029e6ef34b5696 14116 snp-sites_2.5.1-2_armhf.deb
Files:
0d27c7cbe2787eb8b14b722e472ab7c4 20164 debug optional libsnp-sites1-dbgsym_2.5.1-2_armhf.deb
17546f35e61e9ae5e5d5a819241d1e5f 16520 libdevel optional libsnp-sites1-dev_2.5.1-2_armhf.deb
337a0b7d1bafc865130022ef9fabf178 13340 libs optional libsnp-sites1_2.5.1-2_armhf.deb
20d6c20236eb7a36ac39d2a0167ba76e 6496 debug optional snp-sites-dbgsym_2.5.1-2_armhf.deb
8da6ae236f1d36eed1d98c3438803698 7430 science optional snp-sites_2.5.1-2_armhf.buildinfo
6264ae869ff3960c5f6c3fde140fed4d 14116 science optional snp-sites_2.5.1-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libsnp-sites1-dbgsym_2.5.1-2_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 20164 bytes: control archive=552 bytes.
406 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libsnp-sites1-dbgsym
Source: snp-sites
Version: 2.5.1-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 34
Depends: libsnp-sites1 (= 2.5.1-2)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libsnp-sites1
Build-Ids: 93dbd15eaffab8edaa9b5974473fa15ce1fa9253
drwxr-xr-x root/root 0 2021-10-01 14:16 ./
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/debug/.build-id/93/
-rw-r--r-- root/root 23804 2021-10-01 14:16 ./usr/lib/debug/.build-id/93/dbd15eaffab8edaa9b5974473fa15ce1fa9253.debug
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-01 14:16 ./usr/share/doc/libsnp-sites1-dbgsym -> libsnp-sites1
libsnp-sites1-dev_2.5.1-2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 16520 bytes: control archive=1184 bytes.
971 bytes, 25 lines control
819 bytes, 11 lines md5sums
Package: libsnp-sites1-dev
Source: snp-sites
Version: 2.5.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 60
Depends: libsnp-sites1 (= 2.5.1-2)
Conflicts: libsnp-sites-dev
Provides: libsnp-sites-dev
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/sanger-pathogens/snp-sites
Description: Static libraries and header files for the package snp-sites
Snp-sites finds single nucleotide polymorphism (SNP) sites from
multi-fasta alignment input files (which might be compressed). Its
output can be in various widely used formats (Multi Fasta Alignment,
Vcf, phylip).
.
The software has been developed at the Wellcome Trust Sanger Institute.
.
This package contains the development files to include snp-sites
into your own code. The library enables Python developers to make
snp-sites function calls (Python bindings) through the Boost Python
Library.
drwxr-xr-x root/root 0 2021-10-01 14:16 ./
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/include/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/include/snp-sites/
-rw-r--r-- root/root 1487 2021-10-01 14:16 ./usr/include/snp-sites/alignment-file.h
-rw-r--r-- root/root 1145 2021-10-01 14:16 ./usr/include/snp-sites/fasta-of-snp-sites.h
-rw-r--r-- root/root 8809 2021-10-01 14:16 ./usr/include/snp-sites/kseq.h
-rw-r--r-- root/root 1149 2021-10-01 14:16 ./usr/include/snp-sites/phylib-of-snp-sites.h
-rw-r--r-- root/root 2151 2021-10-01 14:16 ./usr/include/snp-sites/snp-sites.h
-rw-r--r-- root/root 2005 2021-10-01 14:16 ./usr/include/snp-sites/vcf.h
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 20114 2021-10-01 14:16 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.a
lrwxrwxrwx root/root 0 2021-10-01 14:16 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so -> libsnp-sites.so.1.0.0
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/doc/libsnp-sites1-dev/
-rw-r--r-- root/root 504 2021-10-01 14:16 ./usr/share/doc/libsnp-sites1-dev/README.Debian
-rw-r--r-- root/root 1299 2021-10-01 14:16 ./usr/share/doc/libsnp-sites1-dev/changelog.Debian.gz
-rw-r--r-- root/root 2542 2019-10-22 10:21 ./usr/share/doc/libsnp-sites1-dev/changelog.gz
-rw-r--r-- root/root 2355 2021-10-01 14:16 ./usr/share/doc/libsnp-sites1-dev/copyright
libsnp-sites1_2.5.1-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 13340 bytes: control archive=996 bytes.
749 bytes, 20 lines control
313 bytes, 4 lines md5sums
40 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: libsnp-sites1
Source: snp-sites
Version: 2.5.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 37
Depends: libc6 (>= 2.4), zlib1g (>= 1:1.1.4)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/sanger-pathogens/snp-sites
Description: Shared libraries of the package snp-sites
Snp-sites finds single nucleotide polymorphism (SNP) sites from
multi-fasta alignment input files (which might be compressed). Its
output can be in various widely used formats (Multi Fasta Alignment,
Vcf, phylip).
.
The software has been developed at the Wellcome Trust Sanger Institute.
.
This package contains the dynamic library uses by snp-sites.
drwxr-xr-x root/root 0 2021-10-01 14:16 ./
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2021-10-01 14:16 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1 -> libsnp-sites.so.1.0.0
-rw-r--r-- root/root 17668 2021-10-01 14:16 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/doc/libsnp-sites1/
-rw-r--r-- root/root 1299 2021-10-01 14:16 ./usr/share/doc/libsnp-sites1/changelog.Debian.gz
-rw-r--r-- root/root 2542 2019-10-22 10:21 ./usr/share/doc/libsnp-sites1/changelog.gz
-rw-r--r-- root/root 2355 2021-10-01 14:16 ./usr/share/doc/libsnp-sites1/copyright
snp-sites-dbgsym_2.5.1-2_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 6496 bytes: control archive=536 bytes.
377 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: snp-sites-dbgsym
Source: snp-sites
Version: 2.5.1-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 20
Depends: snp-sites (= 2.5.1-2)
Section: debug
Priority: optional
Description: debug symbols for snp-sites
Build-Ids: 92e350900f4b8ccffef7108955ba062139c32244
drwxr-xr-x root/root 0 2021-10-01 14:16 ./
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/lib/debug/.build-id/92/
-rw-r--r-- root/root 9364 2021-10-01 14:16 ./usr/lib/debug/.build-id/92/e350900f4b8ccffef7108955ba062139c32244.debug
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-01 14:16 ./usr/share/doc/snp-sites-dbgsym -> snp-sites
snp-sites_2.5.1-2_armhf.deb
---------------------------
new Debian package, version 2.0.
size 14116 bytes: control archive=1184 bytes.
1149 bytes, 24 lines control
480 bytes, 7 lines md5sums
Package: snp-sites
Version: 2.5.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 37
Depends: libc6 (>= 2.4), libsnp-sites1 (>= 2.5.1)
Section: science
Priority: optional
Homepage: https://github.com/sanger-pathogens/snp-sites
Description: Binary code for the package snp-sites
This program finds single nucleotide polymorphism (SNP) sites from
multi-fasta alignment input files (which might be compressed). Its
output can be in various widely used formats (Multi Fasta Alignment,
Vcf, phylip).
.
The software has been developed at the Wellcome Trust Sanger Institute.
.
A Single Nucleotide - polymorphism (SNP, pronounced snip; plural snips)
is a DNA sequence variation occurring when a Single Nucleotide — A, T, C
or G — in the genome (or other shared sequence) differs between members
of a biological species or paired chromosomes. For example, two
sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA,
contain a difference in a single nucleotide. In this case there are two
alleles. Almost all common SNPs have only two alleles.
drwxr-xr-x root/root 0 2021-10-01 14:16 ./
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/bin/
-rwxr-xr-x root/root 13780 2021-10-01 14:16 ./usr/bin/snp-sites
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/doc/snp-sites/
-rw-r--r-- root/root 378 2021-10-01 14:16 ./usr/share/doc/snp-sites/README.Debian
-rw-r--r-- root/root 2697 2019-10-22 10:21 ./usr/share/doc/snp-sites/README.md.gz
-rw-r--r-- root/root 1299 2021-10-01 14:16 ./usr/share/doc/snp-sites/changelog.Debian.gz
-rw-r--r-- root/root 2542 2019-10-22 10:21 ./usr/share/doc/snp-sites/changelog.gz
-rw-r--r-- root/root 2355 2021-10-01 14:16 ./usr/share/doc/snp-sites/copyright
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-01 14:16 ./usr/share/man/man1/
-rw-r--r-- root/root 1402 2021-10-01 14:16 ./usr/share/man/man1/snp-sites.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 22192
Build-Time: 125
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 458
Job: snp-sites_2.5.1-2
Machine Architecture: armhf
Package: snp-sites
Package-Time: 635
Source-Version: 2.5.1-2
Space: 22192
Status: successful
Version: 2.5.1-2
--------------------------------------------------------------------------------
Finished at 2021-10-05T06:42:29Z
Build needed 00:10:35, 22192k disc space