proteinortho →
6.0.28+dfsg-1 →
armhf → 2021-02-04 05:28:16
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| proteinortho 6.0.28+dfsg-1 (armhf) Thu, 04 Feb 2021 05:14:22 +0000 |
+==============================================================================+
Package: proteinortho
Version: 6.0.28+dfsg-1
Source Version: 6.0.28+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-fd37c751-00f2-4d0d-a38f-72701373f6e8' 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 [12.1 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.1 MB]
Fetched 25.3 MB in 25s (1000 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: '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 520 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.28+dfsg-1 (dsc) [2184 B]
Get:2 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.28+dfsg-1 (tar) [511 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.28+dfsg-1 (diff) [7028 B]
Fetched 520 kB in 0s (1199 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/proteinortho-dX0Ip5/proteinortho-6.0.28+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/proteinortho-dX0Ip5' 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-H1D9VX/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-H1D9VX/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-H1D9VX/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-H1D9VX/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-H1D9VX/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-H1D9VX/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-H1D9VX/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-H1D9VX/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2836 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils krb5-locales libnss-nis libnss-nisplus 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 10 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-H1D9VX/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12585 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), 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-H1D9VX/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-H1D9VX/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-H1D9VX/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-H1D9VX/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-H1D9VX/apt_archive ./ Sources [549 B]
Get:5 copy:/<<BUILDDIR>>/resolver-H1D9VX/apt_archive ./ Packages [610 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional 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
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libgfortran5 libicu67 liblapack-dev liblapack3 liblmdb0 libmagic-mgc
libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libncurses6 libpipeline1
libprocps8 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 mailcap
man-db media-types mime-support ncbi-blast+ ncbi-data po-debconf procps
python3 python3-minimal python3.9 python3.9-minimal
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff liblapack-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv
python3.9-doc binfmt-support
Recommended packages:
med-config curl | wget | lynx libarchive-cpio-perl libgpm2 ca-certificates
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
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libgfortran5 libicu67 liblapack-dev liblapack3 liblmdb0 libmagic-mgc
libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libncurses6 libpipeline1
libprocps8 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 mailcap
man-db media-types mime-support ncbi-blast+ ncbi-data po-debconf procps
python3 python3-minimal python3.9 python3.9-minimal
sbuild-build-depends-proteinortho-dummy
0 upgraded, 56 newly installed, 0 to remove and 10 not upgraded.
Need to get 41.3 MB of archives.
After this operation, 177 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-H1D9VX/apt_archive ./ sbuild-build-depends-proteinortho-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.1-2+rpi1 [790 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.1-2+rpi1 [1623 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.1-1 [37.8 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf media-types all 4.0.0 [30.3 kB]
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Get:13 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.1-2+rpi1 [1658 kB]
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Get:15 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.1-1 [21.0 kB]
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Get:17 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-3 [170 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-3 [32.4 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-3 [509 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
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Get:32 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.2 [189 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.10.0-1 [25.6 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.10.0-1 [15.3 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-3 [162 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210118-1 [163 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-3 [1214 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.2 [1012 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf diamond-aligner armhf 0.9.30-3 [475 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf liblmdb0 armhf 0.9.24-1 [38.7 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libmbedcrypto3 armhf 2.16.9-0.1 [196 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libmbedx509-0 armhf 2.16.9-0.1 [104 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libmbedtls12 armhf 2.16.9-0.1 [132 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf ncbi-blast+ armhf 2.10.1+ds-1+b1 [9302 kB]
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.21-3) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
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update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up ncbi-blast+ (2.10.1+ds-1+b1) ...
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Setting up debhelper (13.3.2) ...
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Processing triggers for libc-bin (2.31-9+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-7+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-9+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.4-1+rpi1
Package versions: adduser_3.118 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-2 binutils_2.35.1-7+rpi1 binutils-arm-linux-gnueabihf_2.35.1-7+rpi1 binutils-common_2.35.1-7+rpi1 bsdextrautils_2.36.1-6 bsdutils_1:2.36.1-6 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.2 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.10.0-1 diamond-aligner_0.9.30-3 diffutils_1:3.7-5 dirmngr_2.2.20-1 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210118-1 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-6 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-6+rpi1 gettext_0.21-3 gettext-base_0.21-3 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_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.18.3-4 libacl1_2.2.53-9 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.1-7+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36.1-6 libbz2-1.0_1.0.8-4 libc-bin_2.31-9+rpi1 libc-dev-bin_2.31-9+rpi1 libc6_2.31-9+rpi1 libc6-dev_2.31-9+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.45.6-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7+rpi1 libctf0_2.35.1-7+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.256 libdebhelper-perl_13.3.2 libdpkg-perl_1.20.7.1+rpi1 libelf1_0.182-3 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-6 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.10.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran5_10.2.1-6+rpi1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 libldap-common_2.4.56+dfsg-1+rpi1 liblmdb0_0.9.24-1 liblz4-1_1.9.3-1+rpi1 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmbedcrypto3_2.16.9-0.1 libmbedtls12_2.16.9-0.1 libmbedx509-0_2.16.9-0.1 libmount1_2.36.1-6 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 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_0.23.22-1 libpam-cap_1:2.44-1 libpam-modules_1.4.0-2 libpam-modules-bin_1.4.0-2 libpam-runtime_1.4.0-2 libpam0g_1.4.0-2 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.0-6 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 libpython3-stdlib_3.9.1-1 libpython3.9-minimal_3.9.1-2+rpi1 libpython3.9-stdlib_3.9.1-2+rpi1 libreadline8_8.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.12-3 libsmartcols1_2.36.1-6 libsqlite3-0_3.34.1-1 libss2_1.45.6-1 libssl1.1_1.1.1i-2 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.2-5+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.2-5+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-6 libxml2_2.9.10+dfsg-6.3 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.10.4-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 mailcap_3.68 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mime-support_3.66 mount_2.36.1-6 ncbi-blast+_2.10.1+ds-1+b1 ncbi-data_6.1.20170106+dfsg1-9 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.0-6 perl-base_5.32.0-6 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.16-5 python3_3.9.1-1 python3-minimal_3.9.1-1 python3.9_3.9.1-2+rpi1 python3.9-minimal_3.9.1-2+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-proteinortho-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2020f-1 util-linux_2.36.1-6 xz-utils_5.2.5-1.0 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.nieHSCOj/trustedkeys.kbx': General error
gpgv: Signature made Mon Feb 1 10:30:18 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./proteinortho_6.0.28+dfsg-1.dsc
dpkg-source: info: extracting proteinortho in /<<BUILDDIR>>/proteinortho-6.0.28+dfsg
dpkg-source: info: unpacking proteinortho_6.0.28+dfsg.orig.tar.xz
dpkg-source: info: unpacking proteinortho_6.0.28+dfsg-1.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-fd37c751-00f2-4d0d-a38f-72701373f6e8
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package proteinortho
dpkg-buildpackage: info: source version 6.0.28+dfsg-1
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-6.0.28+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-6.0.28+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-6.0.28+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 -ffile-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.28+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 -ffile-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.28+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 -ffile-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.28+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 -ffile-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.28+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-6.0.28+dfsg'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.28+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-6.0.28+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg'
mkdir -p /<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin
dh_auto_install -- install PREFIX=/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin
make -j4 install DESTDIR=/<<BUILDDIR>>/proteinortho-6.0.28\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/<<BUILDDIR>>/proteinortho-6.0.28\+dfsg/debian/proteinortho/usr/bin
make[2]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg'
INSTALLING everything to /<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin
'proteinortho6.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl'
'proteinortho' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho'
'src/BUILD/Linux_armv7l/proteinortho_extract_from_graph.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl'
'src/BUILD/Linux_armv7l/proteinortho_formatUsearch.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl'
'src/BUILD/Linux_armv7l/proteinortho_compareProteinorthoGraphs.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl'
'src/BUILD/Linux_armv7l/proteinortho_do_mcl.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl'
'src/BUILD/Linux_armv7l/proteinortho2html.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl'
'src/BUILD/Linux_armv7l/proteinortho2xml.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl'
'src/BUILD/Linux_armv7l/proteinortho_clustering' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering'
'src/BUILD/Linux_armv7l/proteinortho_singletons.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl'
'src/BUILD/Linux_armv7l/proteinortho_ffadj_mcs.py' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py'
'src/BUILD/Linux_armv7l/proteinortho2tree.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl'
'src/BUILD/Linux_armv7l/proteinortho_history.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl'
'src/BUILD/Linux_armv7l/proteinortho_cleanupblastgraph' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph'
'src/BUILD/Linux_armv7l/proteinortho_graphMinusRemovegraph' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph'
'src/BUILD/Linux_armv7l/proteinortho_treeBuilderCore' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_treeBuilderCore'
'src/BUILD/Linux_armv7l/proteinortho_grab_proteins.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl'
'src/BUILD/Linux_armv7l/proteinortho_summary.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl'
Everything installed successfully to /<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin.
If needed you can add /<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/<<BUILDDIR>>/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin'.
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.28+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.28+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-6.0.28+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-6.0.28+dfsg'
dh_fixperms
find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.28+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_clustering 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: package could avoid a useless dependency if debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph debian/proteinortho/usr/bin/proteinortho_clustering debian/proteinortho/usr/bin/proteinortho_treeBuilderCore debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph 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' in '../proteinortho_6.0.28+dfsg-1_armhf.deb'.
dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_6.0.28+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../proteinortho_6.0.28+dfsg-1_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 2021-02-04T05:28:06Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
proteinortho_6.0.28+dfsg-1_armhf.changes:
-----------------------------------------
Format: 1.8
Date: Mon, 01 Feb 2021 15:55:28 +0530
Source: proteinortho
Binary: proteinortho proteinortho-dbgsym
Architecture: armhf
Version: 6.0.28+dfsg-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
proteinortho - Detection of (Co-)orthologs in large-scale protein analysis
Changes:
proteinortho (6.0.28+dfsg-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
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ab92cf7659a503fb6a4456888b2d349762b14de8 5835 proteinortho_6.0.28+dfsg-1_armhf.buildinfo
53788b3e861c2745b0259bc9e25a5f403c225afa 197100 proteinortho_6.0.28+dfsg-1_armhf.deb
Checksums-Sha256:
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fe0570744458210a07552f0da4ff8484b5e57bbff8b54d6bf849c288adb51939 5835 proteinortho_6.0.28+dfsg-1_armhf.buildinfo
26204537210ef61036179e4aeac0f4ef213e48630bf5d30eac17b11f37f97b1e 197100 proteinortho_6.0.28+dfsg-1_armhf.deb
Files:
b57b7ba229005cb41c1640bc898602c8 895092 debug optional proteinortho-dbgsym_6.0.28+dfsg-1_armhf.deb
2ec98007117f627862ec49c4033328b8 5835 science optional proteinortho_6.0.28+dfsg-1_armhf.buildinfo
8e3f12392056d14ce60b6a3fc405bbea 197100 science optional proteinortho_6.0.28+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
proteinortho-dbgsym_6.0.28+dfsg-1_armhf.deb
-------------------------------------------
new Debian package, version 2.0.
size 895092 bytes: control archive=756 bytes.
525 bytes, 12 lines control
516 bytes, 5 lines md5sums
Package: proteinortho-dbgsym
Source: proteinortho
Version: 6.0.28+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 947
Depends: proteinortho (= 6.0.28+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for proteinortho
Build-Ids: 37315802dce19c01adde6484bff83440606f42bb 4bdf0622ab6f87b95b37ad36ac8d0b735ac506ba 8ff4808013962f407e777bd205de8f3745d000a0 c4f34b6fa11ff43d25d6f417d480b78771170c8b
drwxr-xr-x root/root 0 2021-02-01 10:25 ./
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/lib/
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/lib/debug/.build-id/37/
-rw-r--r-- root/root 104448 2021-02-01 10:25 ./usr/lib/debug/.build-id/37/315802dce19c01adde6484bff83440606f42bb.debug
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/lib/debug/.build-id/4b/
-rw-r--r-- root/root 670388 2021-02-01 10:25 ./usr/lib/debug/.build-id/4b/df0622ab6f87b95b37ad36ac8d0b735ac506ba.debug
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/lib/debug/.build-id/8f/
-rw-r--r-- root/root 132784 2021-02-01 10:25 ./usr/lib/debug/.build-id/8f/f4808013962f407e777bd205de8f3745d000a0.debug
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/lib/debug/.build-id/c4/
-rw-r--r-- root/root 14436 2021-02-01 10:25 ./usr/lib/debug/.build-id/c4/f34b6fa11ff43d25d6f417d480b78771170c8b.debug
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 30544 2021-02-01 10:25 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/proteinortho.debug
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/share/
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-02-01 10:25 ./usr/share/doc/proteinortho-dbgsym -> proteinortho
proteinortho_6.0.28+dfsg-1_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 197100 bytes: control archive=1864 bytes.
968 bytes, 17 lines control
2538 bytes, 35 lines md5sums
Package: proteinortho
Version: 6.0.28+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 730
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 2021-02-01 10:25 ./
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/
drwxr-xr-x root/root 0 2021-02-01 10:25 ./usr/bin/
lrwxrwxrwx root/root 0 2021-02-01 10:25 ./usr/bin/proteinortho -> proteinortho6.pl
-rwxr-xr-x root/root 38221 2021-02-01 10:25 ./usr/bin/proteinortho2html.pl
-rwxr-xr-x root/root 4997 2021-02-01 10:25 ./usr/bin/proteinortho2tree.pl
-rwxr-xr-x root/root 8019 2021-02-01 10:25 ./usr/bin/proteinortho2xml.pl
-rwxr-xr-x root/root 155950 2021-02-01 10:25 ./usr/bin/proteinortho6.pl
-rwxr-xr-x root/root 30356 2021-02-01 10:25 ./usr/bin/proteinortho_cleanupblastgraph
-rwxr-xr-x root/root 116424 2021-02-01 10:25 ./usr/bin/proteinortho_clustering
-rwxr-xr-x root/root 1239 2021-02-01 10:25 ./usr/bin/proteinortho_compareProteinorthoGraphs.pl
-rwxr-xr-x root/root 8787 2021-02-01 10:25 ./usr/bin/proteinortho_do_mcl.pl
-rwxr-xr-x root/root 1166 2021-02-01 10:25 ./usr/bin/proteinortho_extract_from_graph.pl
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Purging /<<BUILDDIR>>
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| Summary |
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Build Architecture: armhf
Build-Space: 9460
Build-Time: 347
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 426
Job: proteinortho_6.0.28+dfsg-1
Machine Architecture: armhf
Package: proteinortho
Package-Time: 824
Source-Version: 6.0.28+dfsg-1
Space: 9460
Status: successful
Version: 6.0.28+dfsg-1
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Finished at 2021-02-04T05:28:06Z
Build needed 00:13:44, 9460k disc space