proteinortho →
6.0.12+dfsg-2 →
armhf → 2020-01-19 05:24:39
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| proteinortho 6.0.12+dfsg-2 (armhf) Sun, 19 Jan 2020 05:10:14 +0000 |
+==============================================================================+
Package: proteinortho
Version: 6.0.12+dfsg-2
Source Version: 6.0.12+dfsg-2
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-0b530933-82b3-4d6b-bec1-c28d55c09eed' 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 [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
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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 295 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.12+dfsg-2 (dsc) [2119 B]
Get:2 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.12+dfsg-2 (tar) [285 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.12+dfsg-2 (diff) [7464 B]
Fetched 295 kB in 0s (4049 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/proteinortho-8p9v9j/proteinortho-6.0.12+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/proteinortho-8p9v9j' 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-PYpI2M/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-PYpI2M/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-PYpI2M/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-PYpI2M/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-PYpI2M/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-PYpI2M/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-PYpI2M/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-PYpI2M/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2653 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 1 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-PYpI2M/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 ... 12210 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 (= 12), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner, procps
Filtered Build-Depends: debhelper-compat (= 12), ncbi-blast+, liblapack-dev, diamond-aligner, procps
dpkg-deb: building package 'sbuild-build-depends-proteinortho-dummy' in '/<<BUILDDIR>>/resolver-PYpI2M/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-PYpI2M/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-PYpI2M/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-PYpI2M/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-PYpI2M/apt_archive ./ Sources [548 B]
Get:5 copy:/<<BUILDDIR>>/resolver-PYpI2M/apt_archive ./ Packages [609 B]
Fetched 2490 B in 1s (3113 B/s)
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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism diamond-aligner dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblas-dev
libblas3 libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libicu63
liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3
libmbedtls12 libmbedx509-0 libmpdec2 libncurses6 libpipeline1 libprocps7
libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libsigsegv2
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db mime-support ncbi-blast+ ncbi-data po-debconf procps python3
python3-minimal python3.7 python3.7-minimal sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation 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 python3.7-venv python3.7-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 bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism diamond-aligner dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblas-dev
libblas3 libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libicu63
liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3
libmbedtls12 libmbedx509-0 libmpdec2 libncurses6 libpipeline1 libprocps7
libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libsigsegv2
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db mime-support ncbi-blast+ ncbi-data po-debconf procps python3
python3-minimal python3.7 python3.7-minimal
sbuild-build-depends-proteinortho-dummy sensible-utils
0 upgraded, 62 newly installed, 0 to remove and 1 not upgraded.
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Get:1 copy:/<<BUILDDIR>>/resolver-PYpI2M/apt_archive ./ sbuild-build-depends-proteinortho-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
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Get:20 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libprocps7 armhf 2:3.3.15-2 [58.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.15-2 [235 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-3 [262 kB]
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Get:26 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-3 [66.8 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
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Get:31 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
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Get:37 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
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Get:43 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1 [1138 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.3 [1019 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf diamond-aligner armhf 0.9.22+dfsg-2 [438 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
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Get:55 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-1 [1597 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-1 [2981 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf liblmdb0 armhf 0.9.22-1 [38.2 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libmbedcrypto3 armhf 2.16.3-1 [192 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libmbedx509-0 armhf 2.16.3-1 [99.2 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libmbedtls12 armhf 2.16.3-1 [125 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf ncbi-data all 6.1.20170106+dfsg1-7 [3555 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf ncbi-blast+ armhf 2.8.1-2+b1 [9008 kB]
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libncurses6:armhf (6.1+20191019-1) ...
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update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
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Setting up libsub-override-perl (0.09-2) ...
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Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up liblapack-dev:armhf (3.9.0-1) ...
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
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
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Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libpython3-stdlib:armhf (3.7.5-3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.7 (3.7.6-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up python3 (3.7.5-3) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up ncbi-blast+ (2.8.1-2+b1) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.7.3) ...
Setting up sbuild-build-depends-proteinortho-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-7+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_2.33.1-6+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-22+rpi1 gcc-9_9.2.1-22+rpi1 libc6-dev_2.29-7+rpi1 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.1-6+rpi1 binutils-arm-linux-gnueabihf_2.33.1-6+rpi1 binutils-common_2.33.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-22+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-1 diamond-aligner_0.9.22+dfsg-2 diffutils_1:3.7-3 dirmngr_2.2.19-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-3 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-22+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-3+b1 gcc-8-base_8.3.0-26+rpi1 gcc-9_9.2.1-22+rpi1 gcc-9-base_9.2.1-22+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-22+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-22+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-6+rpi1 libblas-dev_3.9.0-1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-7+rpi1 libc-dev-bin_2.29-7+rpi1 libc6_2.29-7+rpi1 libc6-dev_2.29-7+rpi1 libcap-ng0_0.7.9-2.1 libcc1-0_9.2.1-22+rpi1 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-22+rpi1 libgcc1_1:9.2.1-22+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-22+rpi1 libglib2.0-0_2.62.4-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-22+rpi1 libgpg-error0_1.36-7 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libksba8_1.3.5-2 liblapack-dev_3.9.0-1 liblapack3_3.9.0-1 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblmdb0_0.9.22-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-3 libmagic1_1:5.38-3 libmbedcrypto3_2.16.3-1 libmbedtls12_2.16.3-1 libmbedx509-0_2.16.3-1 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libprocps7_2:3.3.15-2 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1 libpython3.7-stdlib_3.7.6-1 libreadline8_8.0-3 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1+fossil191229-1 libss2_1.45.5-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 libsub-override-perl_0.09-2 libsystemd0_244-3+rpi1+b1 libtasn1-6_4.15.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-22+rpi1 libuchardet0_0.0.6-3 libudev1_244-3+rpi1+b1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncbi-blast+_2.8.1-2+b1 ncbi-data_6.1.20170106+dfsg1-7 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 procps_2:3.3.15-2 python3_3.7.5-3 python3-minimal_3.7.5-3 python3.7_3.7.6-1 python3.7-minimal_3.7.6-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 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_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jan 13 12:13:15 2020 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./proteinortho_6.0.12+dfsg-2.dsc
dpkg-source: info: extracting proteinortho in /<<BUILDDIR>>/proteinortho-6.0.12+dfsg
dpkg-source: info: unpacking proteinortho_6.0.12+dfsg.orig.tar.xz
dpkg-source: info: unpacking proteinortho_6.0.12+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying python3
dpkg-source: info: applying hardening
dpkg-source: info: applying deb_diamond
dpkg-source: info: applying spelling
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-0b530933-82b3-4d6b-bec1-c28d55c09eed
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 6.0.12+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.12+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[2]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
rm -f remove.graph test_blastp.blast-graph test_blastp.info test_blastp.proteinortho-graph test_blastp.proteinortho-graph.summary test_blastp.proteinortho.html test_blastp.proteinortho.tsv test_lastp.blast-graph test_lastp.info test_lastp.proteinortho-graph test_lastp.proteinortho-graph.summary test_lastp.proteinortho.html test_lastp.proteinortho.tsv test_synteny.blast-graph test_synteny.ffadj-graph test_synteny.info test_synteny.poff-graph test_synteny.poff.html test_synteny.poff.tsv test_synteny.proteinortho-graph test_synteny.proteinortho-graph.summary test_synteny.proteinortho.html test_synteny.proteinortho.tsv test_synteny.poff-graph.summary
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
Creating build directory ...
[ 10%] Prepare proteinortho_clustering ...
[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wno-unused-result -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 && ([ $? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX)."; \
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wno-unused-result -fopenmp -o src/BUILD/Linux_armv7l/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -lpthread && ([ $? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas."; \
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wno-unused-result -fopenmp -o src/BUILD/Linux_armv7l/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -lopenblas -pthread -lpthread && ([ $? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking."; \
echo "......[ 33%] Extracting the LAPACK library"; \
if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \
if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=g++ > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wno-unused-result -fopenmp -o src/BUILD/Linux_armv7l/proteinortho_clustering src/proteinortho_clustering.cpp -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas -Wl,-z,relro -Wl,-z,now -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) )
[ 25%] Building **graphMinusRemovegraph**
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wno-unused-result -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-6.0.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wno-unused-result -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-6.0.12+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++/9/vector:72,
from src/proteinortho_clustering.cpp:24:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ConnectedComponent&}; _Tp = ConnectedComponent; _Alloc = std::allocator<ConnectedComponent>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ConnectedComponent>::iterator' {aka '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/proteinortho_clustering.cpp:22:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/9/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++/9/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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/proteinortho_clustering.cpp:22:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Distance = int; _Tp = ConnectedComponent; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from src/proteinortho_clustering.cpp:22:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/proteinortho_clustering.cpp:24:
/usr/include/c++/9/bits/stl_vector.h: In function 'void partition_graph()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/proteinortho_clustering.cpp:22:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
......OK dynamic linking was successful for proteinortho_clustering!
[100%] Everything is compiled with no errors.
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
[TEST] Clean up all test files...
[TEST] Clean up all test files...
[TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped)
[1/12] -p=blastp+ test:
passed
[2/12] -p=blastp+ synteny (PoFF) test:
[STDERR] Error: wrong fromat... Please make sure you only provide *.blast-graph or *.proteinortho-graph files as input...
Died at .//src/BUILD/Linux_armv7l/proteinortho_summary.pl line 117, <$FH> line 2.
passed
[3/12] -p=diamond test:
!!!!
WARNING 'diamond' version 0.9.22 has a known bug that incorrectly computes the length of an alignment, thus the coverage threshold can produce wrong results leading in false negatives. See https://gitlab.com/paulklemm_PHD/proteinortho/issues/24 for more details.
>>> Please update diamond to 0.9.29 or higher <<<
Press 'strg+c' to prevent me from proceeding or wait 10 seconds to continue...
!!!
Well then, proceeding...
passed
[4/12] -p=diamond (--moresensitive) test (subparaBlast): diamond missing, skipping...
[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=blastp (legacy blast) test: blastall missing, skipping...
[TEST] 2. -step=3 tests (proteinortho_clustering)
[1/2] various test functions of proteinortho_clustering (-test): passed
[2/2] Compare results of 'with lapack' and 'without lapack': passed
[TEST] All tests passed
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
dh_auto_install --buildsystem=makefile -- install PREFIX=/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho
make -j4 install DESTDIR=/<<BUILDDIR>>/proteinortho-6.0.12\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/<<BUILDDIR>>/proteinortho-6.0.12\+dfsg/debian/proteinortho/usr/lib/proteinortho
make[2]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
INSTALLING everything to /<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho
'proteinortho6.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho6.pl'
'proteinortho' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho'
'src/BUILD/Linux_armv7l/proteinortho_extract_from_graph.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_extract_from_graph.pl'
'src/BUILD/Linux_armv7l/proteinortho_formatUsearch.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_formatUsearch.pl'
'src/BUILD/Linux_armv7l/proteinortho_compareProteinorthoGraphs.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_compareProteinorthoGraphs.pl'
'src/BUILD/Linux_armv7l/proteinortho_do_mcl.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_do_mcl.pl'
'src/BUILD/Linux_armv7l/proteinortho2html.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho2html.pl'
'src/BUILD/Linux_armv7l/proteinortho2xml.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho2xml.pl'
'src/BUILD/Linux_armv7l/proteinortho_clustering' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_clustering'
'src/BUILD/Linux_armv7l/proteinortho_singletons.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_singletons.pl'
'src/BUILD/Linux_armv7l/proteinortho_ffadj_mcs.py' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_ffadj_mcs.py'
'src/BUILD/Linux_armv7l/proteinortho2tree.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho2tree.pl'
'src/BUILD/Linux_armv7l/proteinortho_history.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_history.pl'
'src/BUILD/Linux_armv7l/proteinortho_cleanupblastgraph' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_cleanupblastgraph'
'src/BUILD/Linux_armv7l/proteinortho_graphMinusRemovegraph' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_graphMinusRemovegraph'
'src/BUILD/Linux_armv7l/proteinortho_treeBuilderCore' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_treeBuilderCore'
'src/BUILD/Linux_armv7l/proteinortho_grab_proteins.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_grab_proteins.pl'
'src/BUILD/Linux_armv7l/proteinortho_summary.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho_summary.pl'
Everything installed successfully to /<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho.
If needed you can add /<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho to $PATH with 'export PATH=$PATH:/<<BUILDDIR>>/proteinortho-6.0.12+dfsg/debian/proteinortho/usr/lib/proteinortho'.
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.12+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-6.0.12+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
dh_fixperms
find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.12+dfsg'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/proteinortho/usr/lib/proteinortho/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/lib/proteinortho/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/lib/proteinortho/proteinortho_graphMinusRemovegraph 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/lib/proteinortho/proteinortho_clustering debian/proteinortho/usr/lib/proteinortho/proteinortho_cleanupblastgraph debian/proteinortho/usr/lib/proteinortho/proteinortho_graphMinusRemovegraph debian/proteinortho/usr/lib/proteinortho/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_6.0.12+dfsg-2_armhf.deb'.
dpkg-deb: building package 'proteinortho' in '../proteinortho_6.0.12+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../proteinortho_6.0.12+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 2020-01-19T05:24:33Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
proteinortho_6.0.12+dfsg-2_armhf.changes:
-----------------------------------------
Format: 1.8
Date: Mon, 13 Jan 2020 13:12:59 +0100
Source: proteinortho
Binary: proteinortho proteinortho-dbgsym
Architecture: armhf
Version: 6.0.12+dfsg-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
proteinortho - Detection of (Co-)orthologs in large-scale protein analysis
Changes:
proteinortho (6.0.12+dfsg-2) unstable; urgency=medium
.
* Team upload.
* patch: Use #!/usr/bin/python3 (fixes autopkgtests)
* patch: Find the packaged version of the Diamond aligner in
/usr/lib/debian-med/bin, which will help with backports
* patch: Improve build hardening via CPPFLAGS & CFLAGS
* Expanded autopkgtests, following `make test`
* patch: fix a spelling typo
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Checksums-Sha256:
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Files:
05527659650ffbf3b69778af9e6c4542 952256 debug optional proteinortho-dbgsym_6.0.12+dfsg-2_armhf.deb
151ec44e1deb0bb6a374619d18d7d603 5479 science optional proteinortho_6.0.12+dfsg-2_armhf.buildinfo
df70f9bef32438d55da022f76f93d6d0 195448 science optional proteinortho_6.0.12+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
proteinortho-dbgsym_6.0.12+dfsg-2_armhf.deb
-------------------------------------------
new Debian package, version 2.0.
size 952256 bytes: control archive=764 bytes.
526 bytes, 12 lines control
516 bytes, 5 lines md5sums
Package: proteinortho-dbgsym
Source: proteinortho
Version: 6.0.12+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1000
Depends: proteinortho (= 6.0.12+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for proteinortho
Build-Ids: 8b009bbe8b055e8b532c238ea41ba18250fefc82 8dd70767bf2db37352e973821ca79820d060d641 98969b3ad6713bcd6557cdc1bfe75221eb968aa5 e34ac2dc2a0ec34e4f107b87764a611865e2163e
drwxr-xr-x root/root 0 2020-01-13 12:12 ./
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drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/lib/debug/.build-id/8b/
-rw-r--r-- root/root 133260 2020-01-13 12:12 ./usr/lib/debug/.build-id/8b/009bbe8b055e8b532c238ea41ba18250fefc82.debug
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/lib/debug/.build-id/8d/
-rw-r--r-- root/root 718492 2020-01-13 12:12 ./usr/lib/debug/.build-id/8d/d70767bf2db37352e973821ca79820d060d641.debug
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/lib/debug/.build-id/98/
-rw-r--r-- root/root 13612 2020-01-13 12:12 ./usr/lib/debug/.build-id/98/969b3ad6713bcd6557cdc1bfe75221eb968aa5.debug
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-rw-r--r-- root/root 108280 2020-01-13 12:12 ./usr/lib/debug/.build-id/e3/4ac2dc2a0ec34e4f107b87764a611865e2163e.debug
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 31856 2020-01-13 12:12 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/proteinortho.debug
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/share/
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-01-13 12:12 ./usr/share/doc/proteinortho-dbgsym -> proteinortho
proteinortho_6.0.12+dfsg-2_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 195448 bytes: control archive=1864 bytes.
968 bytes, 17 lines control
2808 bytes, 36 lines md5sums
Package: proteinortho
Version: 6.0.12+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 840
Depends: libc6 (>= 2.7), libgcc1 (>= 1:3.5), 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 2020-01-13 12:12 ./
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/bin/
lrwxrwxrwx root/root 0 2020-01-13 12:12 ./usr/bin/proteinortho -> proteinortho6
-rwxr-xr-x root/root 52 2020-01-13 10:30 ./usr/bin/proteinortho6
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/lib/
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/lib/proteinortho/
-rwxr-xr-x root/root 137260 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho
-rwxr-xr-x root/root 36280 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho2html.pl
-rwxr-xr-x root/root 4997 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho2tree.pl
-rwxr-xr-x root/root 4697 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho2xml.pl
-rwxr-xr-x root/root 137260 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho6.pl
-rwxr-xr-x root/root 30356 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_cleanupblastgraph
-rwxr-xr-x root/root 124616 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_clustering
-rwxr-xr-x root/root 1239 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_compareProteinorthoGraphs.pl
-rwxr-xr-x root/root 8787 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_do_mcl.pl
-rwxr-xr-x root/root 1166 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_extract_from_graph.pl
-rwxr-xr-x root/root 32953 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_ffadj_mcs.py
-rwxr-xr-x root/root 479 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_formatUsearch.pl
-rwxr-xr-x root/root 10913 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_grab_proteins.pl
-rwxr-xr-x root/root 22164 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_graphMinusRemovegraph
-rwxr-xr-x root/root 27858 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_history.pl
-rwxr-xr-x root/root 1616 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_singletons.pl
-rwxr-xr-x root/root 10921 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_summary.pl
-rwxr-xr-x root/root 9824 2020-01-13 12:12 ./usr/lib/proteinortho/proteinortho_treeBuilderCore
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/share/
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/share/doc/proteinortho/
-rw-r--r-- root/root 263 2020-01-13 10:30 ./usr/share/doc/proteinortho/README.test
-rw-r--r-- root/root 1075 2020-01-13 12:12 ./usr/share/doc/proteinortho/changelog.Debian.gz
-rw-r--r-- root/root 6146 2019-12-12 08:03 ./usr/share/doc/proteinortho/changelog.gz
-rw-r--r-- root/root 1081 2020-01-13 10:30 ./usr/share/doc/proteinortho/copyright
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/share/doc/proteinortho/examples/
-rw-r--r-- root/root 52855 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/C.faa
-rw-r--r-- root/root 18467 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/C.gff
-rw-r--r-- root/root 751 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/C2.faa
-rw-r--r-- root/root 120 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/C2.gff
-rw-r--r-- root/root 55942 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/E.faa
-rw-r--r-- root/root 18666 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/E.gff
-rw-r--r-- root/root 27375 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/L.faa
-rw-r--r-- root/root 2376 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/L.gff
-rw-r--r-- root/root 27690 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/M.faa
-rw-r--r-- root/root 2317 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/M.gff
-rwxr-xr-x root/root 262 2019-12-12 08:03 ./usr/share/doc/proteinortho/examples/chk_test.pl
-rw-r--r-- root/root 2281 2020-01-13 11:38 ./usr/share/doc/proteinortho/run-unit-test
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/share/man/
drwxr-xr-x root/root 0 2020-01-13 12:12 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2020-01-13 12:12 ./usr/share/man/man1/proteinortho.1.gz -> proteinortho6.1.gz
-rw-r--r-- root/root 1562 2020-01-13 12:12 ./usr/share/man/man1/proteinortho6.1.gz
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| Post Build |
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| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 9480
Build-Time: 312
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 499
Job: proteinortho_6.0.12+dfsg-2
Machine Architecture: armhf
Package: proteinortho
Package-Time: 859
Source-Version: 6.0.12+dfsg-2
Space: 9480
Status: successful
Version: 6.0.12+dfsg-2
--------------------------------------------------------------------------------
Finished at 2020-01-19T05:24:33Z
Build needed 00:14:19, 9480k disc space