Raspbian Package Auto-Building

Build log for proteinortho (6.0.14+dfsg-1) on armhf

proteinortho6.0.14+dfsg-1armhf → 2020-02-21 05:23:27

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02

+==============================================================================+
| proteinortho 6.0.14+dfsg-1 (armhf)           Fri, 21 Feb 2020 05:09:51 +0000 |
+==============================================================================+

Package: proteinortho
Version: 6.0.14+dfsg-1
Source Version: 6.0.14+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-8d67d324-4ebb-4244-878d-2764cac108b5' 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 [12.7 MB]
Fetched 24.3 MB in 26s (939 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 332 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.14+dfsg-1 (dsc) [2119 B]
Get:2 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.14+dfsg-1 (tar) [322 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.14+dfsg-1 (diff) [7520 B]
Fetched 332 kB in 0s (4420 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/proteinortho-Kp3Wt6/proteinortho-6.0.14+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/proteinortho-Kp3Wt6' 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-QTLCAr/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-QTLCAr/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-QTLCAr/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-QTLCAr/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QTLCAr/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QTLCAr/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QTLCAr/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QTLCAr/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2622 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:
  libpam-cap netbase
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 27 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-QTLCAr/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12256 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-QTLCAr/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-QTLCAr/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QTLCAr/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QTLCAr/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QTLCAr/apt_archive ./ Sources [548 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QTLCAr/apt_archive ./ Packages [611 B]
Fetched 2492 B in 1s (3279 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 packages were automatically installed and are no longer required:
  libpam-cap netbase
Use 'apt autoremove' to remove them.
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 27 not upgraded.
Need to get 43.3 MB of archives.
After this operation, 186 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-QTLCAr/apt_archive ./ sbuild-build-depends-proteinortho-dummy 0.invalid.0 [896 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]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.6-1+b1 [585 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.6-1+b1 [1525 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-3 [36.8 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.6-1+b1 [1669 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.6-1+b1 [351 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-3 [20.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-3 [62.1 kB]
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 1:5.38-4 [262 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 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]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
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]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.9 [183 kB]
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 1.6.3-2 [23.7 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-2 [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 12.9 [994 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf diamond-aligner armhf 0.9.29+dfsg-5 [401 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-1 [113 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-25+rpi1 [231 kB]
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 2.16.4-1 [193 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libmbedx509-0 armhf 2.16.4-1 [100 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libmbedtls12 armhf 2.16.4-1 [126 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf ncbi-data all 6.1.20170106+dfsg1-8 [3552 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf ncbi-blast+ armhf 2.9.0-4 [9088 kB]
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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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/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.7 (3.7.6-1+b1) ...
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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+ (2.9.0-4) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.9) ...
Setting up sbuild-build-depends-proteinortho-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-9+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_2.33.90.20200122-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-25+rpi1 gcc-9_9.2.1-25+rpi1 libc6-dev_2.29-9+rpi1 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 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_2.33.90.20200122-2+rpi1 binutils-arm-linux-gnueabihf_2.33.90.20200122-2+rpi1 binutils-common_2.33.90.20200122-2+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_9.2.1-25+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diamond-aligner_0.9.29+dfsg-5 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_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-25+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_9.2.1-25+rpi1 gcc-9-base_9.2.1-25+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_3.4-1 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 iputils-ping_3:20190709-3 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-25+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-25+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.90.20200122-2+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_2.29-9+rpi1 libc-dev-bin_2.29-9+rpi1 libc6_2.29-9+rpi1 libc6-dev_2.29-9+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-25+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 libctf-nobfd0_2.33.90.20200122-2+rpi1 libctf0_2.33.90.20200122-2+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.9 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 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.2.1-25+rpi1 libgcc1_1:9.2.1-25+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-25+rpi1 libglib2.0-0_2.62.4-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-25+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_1:5.38-4 libmagic1_1:5.38-4 libmbedcrypto3_2.16.4-1 libmbedtls12_2.16.4-1 libmbedx509-0_2.16.4-1 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+b1 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 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+b1 libpython3.7-stdlib_3.7.6-1+b1 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_3.31.0+really3.30.1+fossil191229-1 libss2_1.45.5-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 libsub-override-perl_0.09-2 libsystemd0_244.1-1+rpi1 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_9.2.1-25+rpi1 libuchardet0_0.0.6-3 libudev1_244.1-1+rpi1 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_1.3.4.20200120-1 mime-support_3.64 mount_2.34-0.1 ncbi-blast+_2.9.0-4 ncbi-data_6.1.20170106+dfsg1-8 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+b1 python3.7-minimal_3.7.6-1+b1 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_2.96-2.1 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 Feb 17 13:41:58 2020 UTC
gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./proteinortho_6.0.14+dfsg-1.dsc
dpkg-source: info: extracting proteinortho in /<<BUILDDIR>>/proteinortho-6.0.14+dfsg
dpkg-source: info: unpacking proteinortho_6.0.14+dfsg.orig.tar.xz
dpkg-source: info: unpacking proteinortho_6.0.14+dfsg-1.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-8d67d324-4ebb-4244-878d-2764cac108b5
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package proteinortho
dpkg-buildpackage: info: source version 6.0.14+dfsg-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean
   dh_auto_clean
	make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.14+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-6.0.14+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-6.0.14+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-6.0.14+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-6.0.14+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-6.0.14+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-6.0.14+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-6.0.14+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-6.0.14+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-6.0.14+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-6.0.14+dfsg'
   dh_auto_test -a
	make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.14+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: [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.
USAGE: proteinortho2html.pl <myproject.proteinortho> (<fasta1> <fasta2> ...)
the first argument points to the proteinortho output (tsv)-file. Any further (optional) files should be fasta files, for conversion of the identifier to a proper gene name/ describtion. The HTML output is printed to stdout, use '>' to write the html output to a file.
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=blastp (legacy blast) 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-6.0.14+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-6.0.14+dfsg'
mkdir -p /<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin
dh_auto_install -- install PREFIX=/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin
	make -j4 install DESTDIR=/<<BUILDDIR>>/proteinortho-6.0.14\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/<<BUILDDIR>>/proteinortho-6.0.14\+dfsg/debian/proteinortho/usr/bin
make[2]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg'
INSTALLING everything to /<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin
'proteinortho6.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl'
'proteinortho' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho'
'src/BUILD/Linux_armv7l/proteinortho_extract_from_graph.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl'
'src/BUILD/Linux_armv7l/proteinortho_formatUsearch.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl'
'src/BUILD/Linux_armv7l/proteinortho_compareProteinorthoGraphs.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl'
'src/BUILD/Linux_armv7l/proteinortho_do_mcl.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl'
'src/BUILD/Linux_armv7l/proteinortho2html.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl'
'src/BUILD/Linux_armv7l/proteinortho2xml.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl'
'src/BUILD/Linux_armv7l/proteinortho_clustering' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering'
'src/BUILD/Linux_armv7l/proteinortho_singletons.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl'
'src/BUILD/Linux_armv7l/proteinortho_ffadj_mcs.py' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py'
'src/BUILD/Linux_armv7l/proteinortho2tree.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl'
'src/BUILD/Linux_armv7l/proteinortho_history.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl'
'src/BUILD/Linux_armv7l/proteinortho_cleanupblastgraph' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph'
'src/BUILD/Linux_armv7l/proteinortho_graphMinusRemovegraph' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph'
'src/BUILD/Linux_armv7l/proteinortho_treeBuilderCore' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_treeBuilderCore'
'src/BUILD/Linux_armv7l/proteinortho_grab_proteins.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl'
'src/BUILD/Linux_armv7l/proteinortho_summary.pl' -> '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl'
Everything installed successfully to /<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin.
If needed you can add /<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/<<BUILDDIR>>/proteinortho-6.0.14+dfsg/debian/proteinortho/usr/bin'.
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg'
   debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.14+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-6.0.14+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-6.0.14+dfsg'
dh_fixperms
find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.14+dfsg'
   dh_missing -a
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -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_treeBuilderCore debian/proteinortho/usr/bin/proteinortho_clustering 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_6.0.14+dfsg-1_armhf.deb'.
dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_6.0.14+dfsg-1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../proteinortho_6.0.14+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 2020-02-21T05:23:20Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


proteinortho_6.0.14+dfsg-1_armhf.changes:
-----------------------------------------

Format: 1.8
Date: Mon, 17 Feb 2020 14:29:14 +0100
Source: proteinortho
Binary: proteinortho proteinortho-dbgsym
Architecture: armhf
Version: 6.0.14+dfsg-1
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 (6.0.14+dfsg-1) unstable; urgency=medium
 .
   * Team upload.
   * Install all binaries to /usr/bin/ upon the request of upstream.
Checksums-Sha1:
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 c50ce9d139d0072a3a4501ecc3bd534240d198e8 5627 proteinortho_6.0.14+dfsg-1_armhf.buildinfo
 3503f6cc683b49a5b7bca74b92813bd416deb1c4 197136 proteinortho_6.0.14+dfsg-1_armhf.deb
Checksums-Sha256:
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 a517728ab724e39d62008346f1a47c3a62b02ad790324d540ea370391654154f 5627 proteinortho_6.0.14+dfsg-1_armhf.buildinfo
 83ce0958517ce919c88f2de7774b20729aa994e9c7ccf997d0464b1c1a0162ae 197136 proteinortho_6.0.14+dfsg-1_armhf.deb
Files:
 f7c454b1c3a4a3e301e19c43b02f96a2 951808 debug optional proteinortho-dbgsym_6.0.14+dfsg-1_armhf.deb
 e7a007da84cd87e59a11bd359d5c5e8d 5627 science optional proteinortho_6.0.14+dfsg-1_armhf.buildinfo
 cbdf2cc813b0a73e721a8c6ee79e04da 197136 science optional proteinortho_6.0.14+dfsg-1_armhf.deb

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| Package contents                                                             |
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proteinortho-dbgsym_6.0.14+dfsg-1_armhf.deb
-------------------------------------------

 new Debian package, version 2.0.
 size 951808 bytes: control archive=760 bytes.
     526 bytes,    12 lines      control              
     516 bytes,     5 lines      md5sums              
 Package: proteinortho-dbgsym
 Source: proteinortho
 Version: 6.0.14+dfsg-1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1000
 Depends: proteinortho (= 6.0.14+dfsg-1)
 Section: debug
 Priority: optional
 Description: debug symbols for proteinortho
 Build-Ids: 3269a769b4af528879cf5e60ac8d95e9dbcc794a e190cf4b2a922f0a140ee3ade75db2eaf7b5e18a e548de371a74e35d1beab1270514511cff0238de f76e783c653cd1fa83488d445b1146af63f1e84e

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drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/debug/.build-id/32/
-rw-r--r-- root/root    718488 2020-02-17 13:29 ./usr/lib/debug/.build-id/32/69a769b4af528879cf5e60ac8d95e9dbcc794a.debug
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/debug/.build-id/e1/
-rw-r--r-- root/root    108280 2020-02-17 13:29 ./usr/lib/debug/.build-id/e1/90cf4b2a922f0a140ee3ade75db2eaf7b5e18a.debug
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/debug/.build-id/e5/
-rw-r--r-- root/root    133260 2020-02-17 13:29 ./usr/lib/debug/.build-id/e5/48de371a74e35d1beab1270514511cff0238de.debug
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/debug/.build-id/f7/
-rw-r--r-- root/root     13612 2020-02-17 13:29 ./usr/lib/debug/.build-id/f7/6e783c653cd1fa83488d445b1146af63f1e84e.debug
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root     31856 2020-02-17 13:29 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/proteinortho.debug
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/share/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-02-17 13:29 ./usr/share/doc/proteinortho-dbgsym -> proteinortho


proteinortho_6.0.14+dfsg-1_armhf.deb
------------------------------------

 new Debian package, version 2.0.
 size 197136 bytes: control archive=1832 bytes.
     968 bytes,    17 lines      control              
    2463 bytes,    34 lines      md5sums              
 Package: proteinortho
 Version: 6.0.14+dfsg-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 717
 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 2020-02-17 13:29 ./
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/bin/
lrwxrwxrwx root/root         0 2020-02-17 13:29 ./usr/bin/proteinortho -> proteinortho6.pl
-rwxr-xr-x root/root     38265 2020-02-17 13:29 ./usr/bin/proteinortho2html.pl
-rwxr-xr-x root/root      4997 2020-02-17 13:29 ./usr/bin/proteinortho2tree.pl
-rwxr-xr-x root/root      4697 2020-02-17 13:29 ./usr/bin/proteinortho2xml.pl
-rwxr-xr-x root/root    148841 2020-02-17 13:29 ./usr/bin/proteinortho6.pl
-rwxr-xr-x root/root     30356 2020-02-17 13:29 ./usr/bin/proteinortho_cleanupblastgraph
-rwxr-xr-x root/root    124616 2020-02-17 13:29 ./usr/bin/proteinortho_clustering
-rwxr-xr-x root/root      1239 2020-02-17 13:29 ./usr/bin/proteinortho_compareProteinorthoGraphs.pl
-rwxr-xr-x root/root      8787 2020-02-17 13:29 ./usr/bin/proteinortho_do_mcl.pl
-rwxr-xr-x root/root      1166 2020-02-17 13:29 ./usr/bin/proteinortho_extract_from_graph.pl
-rwxr-xr-x root/root     32953 2020-02-17 13:29 ./usr/bin/proteinortho_ffadj_mcs.py
-rwxr-xr-x root/root       479 2020-02-17 13:29 ./usr/bin/proteinortho_formatUsearch.pl
-rwxr-xr-x root/root     10913 2020-02-17 13:29 ./usr/bin/proteinortho_grab_proteins.pl
-rwxr-xr-x root/root     22164 2020-02-17 13:29 ./usr/bin/proteinortho_graphMinusRemovegraph
-rwxr-xr-x root/root     27858 2020-02-17 13:29 ./usr/bin/proteinortho_history.pl
-rwxr-xr-x root/root      1616 2020-02-17 13:29 ./usr/bin/proteinortho_singletons.pl
-rwxr-xr-x root/root     10921 2020-02-17 13:29 ./usr/bin/proteinortho_summary.pl
-rwxr-xr-x root/root      9824 2020-02-17 13:29 ./usr/bin/proteinortho_treeBuilderCore
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/lib/proteinortho/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/share/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./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      1207 2020-02-17 13:29 ./usr/share/doc/proteinortho/changelog.Debian.gz
-rw-r--r-- root/root      6269 2020-02-06 11:48 ./usr/share/doc/proteinortho/changelog.gz
-rw-r--r-- root/root      1081 2020-02-17 13:29 ./usr/share/doc/proteinortho/copyright
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/share/doc/proteinortho/examples/
-rw-r--r-- root/root     52855 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/C.faa
-rw-r--r-- root/root     18467 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/C.gff
-rw-r--r-- root/root       751 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/C2.faa
-rw-r--r-- root/root       120 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/C2.gff
-rw-r--r-- root/root     55942 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/E.faa
-rw-r--r-- root/root     18666 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/E.gff
-rw-r--r-- root/root     27375 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/L.faa
-rw-r--r-- root/root      2376 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/L.gff
-rw-r--r-- root/root     27690 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/M.faa
-rw-r--r-- root/root      2317 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/M.gff
-rwxr-xr-x root/root       262 2020-02-06 11:48 ./usr/share/doc/proteinortho/examples/chk_test.pl
-rw-r--r-- root/root      2242 2020-02-17 13:29 ./usr/share/doc/proteinortho/run-unit-test
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/share/man/
drwxr-xr-x root/root         0 2020-02-17 13:29 ./usr/share/man/man1/
lrwxrwxrwx root/root         0 2020-02-17 13:29 ./usr/share/man/man1/proteinortho.1.gz -> proteinortho6.1.gz
-rw-r--r-- root/root      1562 2020-02-17 13:29 ./usr/share/man/man1/proteinortho6.1.gz


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| Post Build                                                                   |
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| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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| Summary                                                                      |
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Build Architecture: armhf
Build-Space: 9464
Build-Time: 325
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 437
Job: proteinortho_6.0.14+dfsg-1
Machine Architecture: armhf
Package: proteinortho
Package-Time: 809
Source-Version: 6.0.14+dfsg-1
Space: 9464
Status: successful
Version: 6.0.14+dfsg-1
--------------------------------------------------------------------------------
Finished at 2020-02-21T05:23:20Z
Build needed 00:13:29, 9464k disc space