proteinortho →
6.0.24+dfsg-2 →
armhf → 2020-11-18 05:35:12
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| proteinortho 6.0.24+dfsg-2 (armhf) Wed, 18 Nov 2020 05:14:48 +0000 |
+==============================================================================+
Package: proteinortho
Version: 6.0.24+dfsg-2
Source Version: 6.0.24+dfsg-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-510077e3-e11c-42fb-84f5-db532c9fd757' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.7 MB in 25s (986 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'proteinortho' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/proteinortho.git
Please use:
git clone https://salsa.debian.org/med-team/proteinortho.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 519 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.24+dfsg-2 (dsc) [2144 B]
Get:2 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.24+dfsg-2 (tar) [510 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.24+dfsg-2 (diff) [6964 B]
Fetched 519 kB in 0s (2795 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/proteinortho-wqWjl9/proteinortho-6.0.24+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/proteinortho-wqWjl9' 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-qKHvRn/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-qKHvRn/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-qKHvRn/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-qKHvRn/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2813 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-qKHvRn/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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:
bsdextrautils krb5-locales libpam-cap netbase sensible-utils
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 30 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-qKHvRn/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 (21.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12710 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) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner, procps
Filtered Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev, diamond-aligner, procps
dpkg-deb: building package 'sbuild-build-depends-proteinortho-dummy' in '/<<BUILDDIR>>/resolver-qKHvRn/apt_archive/sbuild-build-depends-proteinortho-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-proteinortho-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-qKHvRn/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Sources [549 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Packages [611 B]
Fetched 2493 B in 1s (3195 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-qKHvRn/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install proteinortho build dependencies (apt-based resolver)
------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev cpp-10 debhelper dh-autoreconf
dh-strip-nondeterminism diamond-aligner dwz file g++-10 gcc-10 gcc-10-base
gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6
libatomic1 libblas-dev libblas3 libcc1-0 libcroco3 libdebhelper-perl libelf1
libexpat1 libfile-stripnondeterminism-perl libgcc-10-dev libgcc-s1
libgfortran5 libglib2.0-0 libgomp1 libicu67 liblapack-dev liblapack3
liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0
libncurses6 libpipeline1 libprocps8 libpython3-stdlib libpython3.8-minimal
libpython3.8-stdlib libsigsegv2 libstdc++-10-dev libstdc++6
libsub-override-perl libtool libubsan1 libuchardet0 libxml2 m4 man-db
mime-support ncbi-blast+ ncbi-data po-debconf procps python3 python3-minimal
python3.8 python3.8-minimal
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-10-locales dh-make
gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev groff liblapack-doc
libstdc++-10-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl python3-doc python3-tk
python3-venv python3.8-venv python3.8-doc binfmt-support
Recommended packages:
med-config curl | wget | lynx libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl
psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism diamond-aligner dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3
libcroco3 libdebhelper-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libicu67
liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3
libmbedtls12 libmbedx509-0 libncurses6 libpipeline1 libprocps8
libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support
ncbi-blast+ ncbi-data po-debconf procps python3 python3-minimal python3.8
python3.8-minimal sbuild-build-depends-proteinortho-dummy
The following packages will be upgraded:
cpp-10 g++-10 gcc-10 gcc-10-base libasan6 libatomic1 libcc1-0 libgcc-10-dev
libgcc-s1 libgomp1 libstdc++-10-dev libstdc++6 libubsan1
13 upgraded, 56 newly installed, 0 to remove and 17 not upgraded.
Need to get 225 MB of archives.
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Get:1 copy:/<<BUILDDIR>>/resolver-qKHvRn/apt_archive ./ sbuild-build-depends-proteinortho-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 10.2.0-16+rpi1 [115 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10.2.0-16+rpi1 [200 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10.2.0-16+rpi1 [36.1 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 10.2.0-16+rpi1 [83.7 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 10.2.0-16+rpi1 [8208 B]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libasan6 armhf 10.2.0-16+rpi1 [301 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf cpp-10 armhf 10.2.0-16+rpi1 [55.6 MB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.2.0-16+rpi1 [31.7 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf g++-10 armhf 10.2.0-16+rpi1 [61.3 MB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gcc-10 armhf 10.2.0-16+rpi1 [62.0 MB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libgcc-10-dev armhf 10.2.0-16+rpi1 [682 kB]
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Get:14 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 10.2.0-16+rpi1 [408 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.6-1 [752 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.6-1 [1552 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.6-1 [37.7 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.6-1 [1654 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.6-1 [422 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.6-1 [20.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.6-1 [64.0 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20200918-1 [79.5 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
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Get:43 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
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Get:50 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.2-1 [1176 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.2 [578 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf diamond-aligner armhf 0.9.30-3 [475 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
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Get:61 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.0-16+rpi1 [232 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
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Get:64 http://172.17.0.1/private bullseye-staging/main armhf liblmdb0 armhf 0.9.24-1 [38.7 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libmbedcrypto3 armhf 2.16.5-1 [194 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libmbedx509-0 armhf 2.16.5-1 [100 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libmbedtls12 armhf 2.16.5-1 [126 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf ncbi-blast+ armhf 2.10.1+ds-1 [9302 kB]
debconf: delaying package configuration, since apt-utils is not installed
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-16+rpi1 gcc-10_10.2.0-16+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc1-2 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-16+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diamond-aligner_0.9.30-3 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-16+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-16+rpi1 gcc-10-base_10.2.0-16+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.17-10 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-16+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-16+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbinutils_2.35.1-2+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-7 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.0-16+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-16+rpi1 libgcc-s1_10.2.0-16+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran5_10.2.0-16+rpi1 libglib2.0-0_2.66.2-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-16+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.53+dfsg-1+rpi1 libldap-common_2.4.53+dfsg-1+rpi1 liblmdb0_0.9.24-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmbedcrypto3_2.16.5-1 libmbedtls12_2.16.5-1 libmbedx509-0_2.16.5-1 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 libpython3-stdlib_3.8.6-1 libpython3.8-minimal_3.8.6-1 libpython3.8-stdlib_3.8.6-1 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.4-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.4-1+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-16+rpi1 libuchardet0_0.0.7-1 libudev1_246.4-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.2 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.36-3 ncbi-blast+_2.10.1+ds-1 ncbi-data_6.1.20170106+dfsg1-9 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 procps_2:3.3.16-5 python3_3.8.6-1 python3-minimal_3.8.6-1 python3.8_3.8.6-1 python3.8-minimal_3.8.6-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-proteinortho-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.6YLhlOpk/trustedkeys.kbx': General error
gpgv: Signature made Sun Nov 15 19:53:58 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./proteinortho_6.0.24+dfsg-2.dsc
dpkg-source: info: extracting proteinortho in /<<BUILDDIR>>/proteinortho-6.0.24+dfsg
dpkg-source: info: unpacking proteinortho_6.0.24+dfsg.orig.tar.xz
dpkg-source: info: unpacking proteinortho_6.0.24+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying deb_diamond
dpkg-source: info: applying baseline.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-510077e3-e11c-42fb-84f5-db532c9fd757
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package proteinortho
dpkg-buildpackage: info: source version 6.0.24+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
rm -rf src/BUILD test/C.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.*
rm -rf src/lapack-3.8.0/
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
Creating build directory ...
[ 10%] Prepare proteinortho_clustering ...
[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)
g++ -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -o src/BUILD/Linux_armv7l/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
[ 25%] Building **graphMinusRemovegraph**
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_armv7l/proteinortho_graphMinusRemovegraph src/graphMinusRemovegraph.cpp -Wl,-z,relro -Wl,-z,now
[ 50%] Building **cleanupblastgraph**
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_armv7l/proteinortho_cleanupblastgraph src/cleanupblastgraph.cpp -Wl,-z,relro -Wl,-z,now
[ 75%] Building **po_tree**
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_armv7l/proteinortho_treeBuilderCore src/po_tree.c -Wl,-z,relro -Wl,-z,now
src/po_tree.c: In function 'fetch_matrix':
src/po_tree.c:330:2: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
330 | fscanf (datei, "%d\n", viecher);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/po_tree.c:341:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
341 | fscanf (datei, "%s ",(*pnamen)[i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/po_tree.c:345:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
345 | fscanf (datei, "%s \n",(*pnamen)[i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/po_tree.c:378:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
378 | fscanf (datei, "%c ",&(matrix[i][*ccs]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/po_tree.c:381:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
381 | fscanf (datei, "%c \n",&(matrix[(*viecher)-1][*ccs]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Distance = int; _Tp = ConnectedComponent; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from src/proteinortho_clustering.cpp:24:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ConnectedComponent&}; _Tp = ConnectedComponent; _Alloc = std::allocator<ConnectedComponent>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ConnectedComponent>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1666 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from src/proteinortho_clustering.cpp:24:
/usr/include/c++/10/bits/stl_vector.h: In function 'void partition_graph()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
- test max_of_diag() : 1
- test generate_random_vector() : 1
- test get_new_x() : 1
- test makeOrthogonal() : 1
- test normalize() : 1
- test getY() : 1
- test splitGroups() : 1
All test passed.
......OK dynamic linking was successful for proteinortho_clustering!
[100%] Everything is compiled with no errors.
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
[TEST] Clean up all test files...
[TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped)
[TEST] Clean up all test files...
[1/12] -p=blastp test: passed
[2/12] -p=blastp+ synteny (PoFF) test:
passed
[3/12] -p=diamond test: passed
[4/12] -p=diamond (--moresensitive) test (subparaBlast): passed
[5/12] -p=lastp (lastal) test: lastal missing, skipping...
[6/12] -p=topaz test: topaz missing, skipping...
[7/12] -p=usearch test: usearch missing, skipping...
[8/12] -p=ublast test: usearch missing, skipping...
[9/12] -p=rapsearch test: rapsearch missing, skipping...
[10/12] -p=blatp (blat) test: blat missing, skipping...
[11/12] -p=mmseqsp (mmseqs) test: mmseqs missing, skipping...
[12/12] -p=autoblast (automatically detect blastp,blastn,...) test: blastall missing, skipping...
[TEST] 2. -step=3 tests (proteinortho_clustering)
[1/2] various test functions of proteinortho_clustering (if this fails, try make clean first): passed
[2/2] Compare results of 'with lapack' and 'without lapack': passed
[TEST] All tests passed
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
mkdir -p /<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin
dh_auto_install -- install PREFIX=/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin
make -j4 install DESTDIR=/<<BUILDDIR>>/proteinortho-6.0.24\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/<<BUILDDIR>>/proteinortho-6.0.24\+dfsg/debian/proteinortho/usr/bin
make[2]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
INSTALLING everything to /<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin
'proteinortho6.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl'
'proteinortho' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho'
'src/BUILD/Linux_armv7l/proteinortho_extract_from_graph.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl'
'src/BUILD/Linux_armv7l/proteinortho_formatUsearch.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl'
'src/BUILD/Linux_armv7l/proteinortho_compareProteinorthoGraphs.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl'
'src/BUILD/Linux_armv7l/proteinortho_do_mcl.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl'
'src/BUILD/Linux_armv7l/proteinortho2html.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl'
'src/BUILD/Linux_armv7l/proteinortho2xml.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl'
'src/BUILD/Linux_armv7l/proteinortho_clustering' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering'
'src/BUILD/Linux_armv7l/proteinortho_singletons.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl'
'src/BUILD/Linux_armv7l/proteinortho_ffadj_mcs.py' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py'
'src/BUILD/Linux_armv7l/proteinortho2tree.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl'
'src/BUILD/Linux_armv7l/proteinortho_history.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl'
'src/BUILD/Linux_armv7l/proteinortho_cleanupblastgraph' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph'
'src/BUILD/Linux_armv7l/proteinortho_graphMinusRemovegraph' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph'
'src/BUILD/Linux_armv7l/proteinortho_treeBuilderCore' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_treeBuilderCore'
'src/BUILD/Linux_armv7l/proteinortho_grab_proteins.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl'
'src/BUILD/Linux_armv7l/proteinortho_summary.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl'
Everything installed successfully to /<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin.
If needed you can add /<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/<<BUILDDIR>>/proteinortho-6.0.24+dfsg/debian/proteinortho/usr/bin'.
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
dh_install
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
dh_fixperms
find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/proteinortho/usr/bin/proteinortho_clustering 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/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph debian/proteinortho/usr/bin/proteinortho_clustering debian/proteinortho/usr/bin/proteinortho_treeBuilderCore were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_6.0.24+dfsg-2_armhf.deb'.
dpkg-deb: building package 'proteinortho' in '../proteinortho_6.0.24+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../proteinortho_6.0.24+dfsg-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 2020-11-18T05:35:02Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
proteinortho_6.0.24+dfsg-2_armhf.changes:
-----------------------------------------
Format: 1.8
Date: Sun, 15 Nov 2020 20:15:41 +0100
Source: proteinortho
Binary: proteinortho proteinortho-dbgsym
Architecture: armhf
Version: 6.0.24+dfsg-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
proteinortho - Detection of (Co-)orthologs in large-scale protein analysis
Closes: 974850
Changes:
proteinortho (6.0.24+dfsg-2) unstable; urgency=medium
.
* Fix baseline violation
Closes: #974850
* No tab in license text (routine-update)
* Lintian override for script-with-language-extension
Checksums-Sha1:
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9e491963714145a2b978dcb939a2f718bac7c256 5837 proteinortho_6.0.24+dfsg-2_armhf.buildinfo
9db0843bf6e19b0e413f43776c2f3ca8897143cd 195756 proteinortho_6.0.24+dfsg-2_armhf.deb
Checksums-Sha256:
7a136d8f90a9044a36279251475d2818c5a7026e43f5faf15e047a12948ff860 895432 proteinortho-dbgsym_6.0.24+dfsg-2_armhf.deb
2ec4fd4212fec2f3100d9865c3312d3f24eb27d1a9da71ad7ca171ac07afd137 5837 proteinortho_6.0.24+dfsg-2_armhf.buildinfo
680d846464726773148f79f51fa5247912d9a9373be92695d4ab5d6453633f35 195756 proteinortho_6.0.24+dfsg-2_armhf.deb
Files:
fbbbd864ce26ac7b5d534d9ac3739495 895432 debug optional proteinortho-dbgsym_6.0.24+dfsg-2_armhf.deb
b67106ee612adc55454472a4d5c2ef32 5837 science optional proteinortho_6.0.24+dfsg-2_armhf.buildinfo
164d8d26b3d21693be30290e592d7169 195756 science optional proteinortho_6.0.24+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
proteinortho-dbgsym_6.0.24+dfsg-2_armhf.deb
-------------------------------------------
new Debian package, version 2.0.
size 895432 bytes: control archive=760 bytes.
525 bytes, 12 lines control
516 bytes, 5 lines md5sums
Package: proteinortho-dbgsym
Source: proteinortho
Version: 6.0.24+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 948
Depends: proteinortho (= 6.0.24+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for proteinortho
Build-Ids: 575a412c7e3bc8a7bd088e8a0e99478d3b7b41e7 8b875145a6acd7af2c03117ac756198bd7cd9d7c 8ee8367b1a78354330c6cf05d3689beb97d9c6ef a269d4b10fee90200c91b82ba6a89fd58ecc424c
drwxr-xr-x root/root 0 2020-11-15 19:15 ./
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/debug/.build-id/57/
-rw-r--r-- root/root 132852 2020-11-15 19:15 ./usr/lib/debug/.build-id/57/5a412c7e3bc8a7bd088e8a0e99478d3b7b41e7.debug
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/debug/.build-id/8b/
-rw-r--r-- root/root 14444 2020-11-15 19:15 ./usr/lib/debug/.build-id/8b/875145a6acd7af2c03117ac756198bd7cd9d7c.debug
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/debug/.build-id/8e/
-rw-r--r-- root/root 670540 2020-11-15 19:15 ./usr/lib/debug/.build-id/8e/e8367b1a78354330c6cf05d3689beb97d9c6ef.debug
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/debug/.build-id/a2/
-rw-r--r-- root/root 104512 2020-11-15 19:15 ./usr/lib/debug/.build-id/a2/69d4b10fee90200c91b82ba6a89fd58ecc424c.debug
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 30532 2020-11-15 19:15 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/proteinortho.debug
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-11-15 19:15 ./usr/share/doc/proteinortho-dbgsym -> proteinortho
proteinortho_6.0.24+dfsg-2_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 195756 bytes: control archive=1864 bytes.
968 bytes, 17 lines control
2538 bytes, 35 lines md5sums
Package: proteinortho
Version: 6.0.24+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 726
Depends: libc6 (>= 2.7), libgcc-s1 (>= 3.5), libgomp1 (>= 6), liblapack3, libstdc++6 (>= 5.2), perl:any, python3, ncbi-blast+, diamond-aligner, procps
Section: science
Priority: optional
Homepage: https://gitlab.com/paulklemm_PHD/proteinortho
Description: Detection of (Co-)orthologs in large-scale protein analysis
Proteinortho is a stand-alone tool that is geared towards large datasets
and makes use of distributed computing techniques when run on multi-core
hardware. It implements an extended version of the reciprocal best
alignment heuristic. Proteinortho was applied to compute orthologous
proteins in the complete set of all 717 eubacterial genomes available at
NCBI at the beginning of 2009. Authors succeeded identifying thirty
proteins present in 99% of all bacterial proteomes.
drwxr-xr-x root/root 0 2020-11-15 19:15 ./
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/bin/
lrwxrwxrwx root/root 0 2020-11-15 19:15 ./usr/bin/proteinortho -> proteinortho6.pl
-rwxr-xr-x root/root 38221 2020-11-15 19:15 ./usr/bin/proteinortho2html.pl
-rwxr-xr-x root/root 4997 2020-11-15 19:15 ./usr/bin/proteinortho2tree.pl
-rwxr-xr-x root/root 8019 2020-11-15 19:15 ./usr/bin/proteinortho2xml.pl
-rwxr-xr-x root/root 153729 2020-11-15 19:15 ./usr/bin/proteinortho6.pl
-rwxr-xr-x root/root 30356 2020-11-15 19:15 ./usr/bin/proteinortho_cleanupblastgraph
-rwxr-xr-x root/root 116424 2020-11-15 19:15 ./usr/bin/proteinortho_clustering
-rwxr-xr-x root/root 1239 2020-11-15 19:15 ./usr/bin/proteinortho_compareProteinorthoGraphs.pl
-rwxr-xr-x root/root 8787 2020-11-15 19:15 ./usr/bin/proteinortho_do_mcl.pl
-rwxr-xr-x root/root 1166 2020-11-15 19:15 ./usr/bin/proteinortho_extract_from_graph.pl
-rwxr-xr-x root/root 32957 2020-11-15 19:15 ./usr/bin/proteinortho_ffadj_mcs.py
-rwxr-xr-x root/root 479 2020-11-15 19:15 ./usr/bin/proteinortho_formatUsearch.pl
-rwxr-xr-x root/root 11372 2020-11-15 19:15 ./usr/bin/proteinortho_grab_proteins.pl
-rwxr-xr-x root/root 26260 2020-11-15 19:15 ./usr/bin/proteinortho_graphMinusRemovegraph
-rwxr-xr-x root/root 27858 2020-11-15 19:15 ./usr/bin/proteinortho_history.pl
-rwxr-xr-x root/root 2169 2020-11-15 19:15 ./usr/bin/proteinortho_singletons.pl
-rwxr-xr-x root/root 10902 2020-11-15 19:15 ./usr/bin/proteinortho_summary.pl
-rwxr-xr-x root/root 9824 2020-11-15 19:15 ./usr/bin/proteinortho_treeBuilderCore
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/lib/proteinortho/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/doc/proteinortho/
-rw-r--r-- root/root 263 2020-11-15 19:15 ./usr/share/doc/proteinortho/README.test
-rw-r--r-- root/root 1505 2020-11-15 19:15 ./usr/share/doc/proteinortho/changelog.Debian.gz
-rw-r--r-- root/root 6915 2020-10-12 14:35 ./usr/share/doc/proteinortho/changelog.gz
-rw-r--r-- root/root 1095 2020-11-15 19:15 ./usr/share/doc/proteinortho/copyright
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/doc/proteinortho/examples/
-rw-r--r-- root/root 52855 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/C.faa
-rw-r--r-- root/root 18467 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/C.gff
-rw-r--r-- root/root 751 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/C2.faa
-rw-r--r-- root/root 120 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/C2.gff
-rw-r--r-- root/root 55942 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/E.faa
-rw-r--r-- root/root 18666 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/E.gff
-rw-r--r-- root/root 27375 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/L.faa
-rw-r--r-- root/root 2376 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/L.gff
-rw-r--r-- root/root 27690 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/M.faa
-rw-r--r-- root/root 2317 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/M.gff
-rwxr-xr-x root/root 262 2020-10-12 14:35 ./usr/share/doc/proteinortho/examples/chk_test.pl
-rw-r--r-- root/root 2242 2020-11-15 19:15 ./usr/share/doc/proteinortho/run-unit-test
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/lintian/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 213 2020-11-15 19:15 ./usr/share/lintian/overrides/proteinortho
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/man/
drwxr-xr-x root/root 0 2020-11-15 19:15 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2020-11-15 19:15 ./usr/share/man/man1/proteinortho.1.gz -> proteinortho6.1.gz
-rw-r--r-- root/root 1562 2020-11-15 19:15 ./usr/share/man/man1/proteinortho6.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 9428
Build-Time: 438
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 723
Job: proteinortho_6.0.24+dfsg-2
Machine Architecture: armhf
Package: proteinortho
Package-Time: 1214
Source-Version: 6.0.24+dfsg-2
Space: 9428
Status: successful
Version: 6.0.24+dfsg-2
--------------------------------------------------------------------------------
Finished at 2020-11-18T05:35:02Z
Build needed 00:20:14, 9428k disc space