Raspbian Package Auto-Building

Build log for proteinortho (6.0.24+dfsg-1) on armhf

proteinortho6.0.24+dfsg-1armhf → 2020-10-23 03:49:53

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+==============================================================================+
| proteinortho 6.0.24+dfsg-1 (armhf)           Fri, 23 Oct 2020 03:39:56 +0000 |
+==============================================================================+

Package: proteinortho
Version: 6.0.24+dfsg-1
Source Version: 6.0.24+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-943a8276-11d0-40e2-8984-7845dbb6026c' 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 [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.5 MB in 9s (2673 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 518 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.24+dfsg-1 (dsc) [2148 B]
Get:2 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.24+dfsg-1 (tar) [510 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main proteinortho 6.0.24+dfsg-1 (diff) [6116 B]
Fetched 518 kB in 0s (3173 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/proteinortho-h0veOe/proteinortho-6.0.24+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/proteinortho-h0veOe' 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-7SgBLu/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-7SgBLu/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-7SgBLu/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-7SgBLu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (8878 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  bsdextrautils libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 54 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (62.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12498 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner, procps
Filtered Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev, diamond-aligner, procps
dpkg-deb: building package 'sbuild-build-depends-proteinortho-dummy' in '/<<BUILDDIR>>/resolver-7SgBLu/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-7SgBLu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ Sources [549 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ Packages [611 B]
Fetched 2493 B in 0s (11.0 kB/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 binutils
  binutils-arm-linux-gnueabihf binutils-common cpp-10 debhelper dh-autoreconf
  dh-strip-nondeterminism diamond-aligner dwz file g++-10 gcc-10 gcc-10-base
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6
  libatomic1 libbinutils libblas-dev libblas3 libcc1-0 libcroco3 libctf0
  libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
  libgcc-10-dev libgcc-s1 libgfortran5 libglib2.0-0 libgomp1 libicu67
  liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3
  libmbedtls12 libmbedx509-0 libncurses6 libncursesw6 libpipeline1 libprocps8
  libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2
  libssl1.1 libstdc++-10-dev libstdc++6 libsub-override-perl libtinfo6 libtool
  libubsan1 libuchardet0 libxml2 m4 man-db mime-support ncbi-blast+ ncbi-data
  po-debconf procps python3 python3-minimal python3.8 python3.8-minimal
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-10-locales
  dh-make gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev groff
  liblapack-doc libstdc++-10-doc libtool-doc gfortran | fortran95-compiler
  gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc
  python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support
Recommended packages:
  med-config curl | wget | lynx libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl
  psmisc
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev debhelper dh-autoreconf
  dh-strip-nondeterminism diamond-aligner dwz file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3
  libcroco3 libdebhelper-perl libelf1 libexpat1
  libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libicu67
  liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3
  libmbedtls12 libmbedx509-0 libncurses6 libpipeline1 libprocps8
  libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2
  libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
  mime-support ncbi-blast+ ncbi-data po-debconf procps python3 python3-minimal
  python3.8 python3.8-minimal sbuild-build-depends-proteinortho-dummy
The following packages will be upgraded:
  binutils binutils-arm-linux-gnueabihf binutils-common cpp-10 g++-10 gcc-10
  gcc-10-base libasan6 libatomic1 libbinutils libcc1-0 libctf0 libgcc-10-dev
  libgcc-s1 libgomp1 libncursesw6 libstdc++-10-dev libstdc++6 libtinfo6
  libubsan1
20 upgraded, 57 newly installed, 0 to remove and 34 not upgraded.
Need to get 75.9 MB/77.2 MB of archives.
After this operation, 183 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7SgBLu/apt_archive ./ sbuild-build-depends-proteinortho-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.2.0-13+rpi1 [31.7 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libctf0 armhf 2.35.1-2+rpi1 [35.3 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf binutils-arm-linux-gnueabihf armhf 2.35.1-2+rpi1 [1710 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libbinutils armhf 2.35.1-2+rpi1 [314 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf binutils-common armhf 2.35.1-2+rpi1 [2215 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf binutils armhf 2.35.1-2+rpi1 [60.2 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10.2.0-13+rpi1 [199 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10.2.0-13+rpi1 [36.1 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 10.2.0-13+rpi1 [84.1 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 10.2.0-13+rpi1 [8180 B]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libasan6 armhf 10.2.0-13+rpi1 [301 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 10.2.0-13+rpi1 [115 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf g++-10 armhf 10.2.0-13+rpi1 [6792 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-10-dev armhf 10.2.0-13+rpi1 [1746 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libgcc-10-dev armhf 10.2.0-13+rpi1 [685 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf gcc-10 armhf 10.2.0-13+rpi1 [12.3 MB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf cpp-10 armhf 10.2.0-13+rpi1 [6249 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 10.2.0-13+rpi1 [409 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.6-1 [752 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.6-1 [1552 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.2-3 [37.6 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20200918-1 [327 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20200918-1 [105 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.6-1 [1654 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.6-1 [422 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.2-3 [20.8 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.2-3 [63.7 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20200918-1 [79.5 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.181-1 [161 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.1-1 [1174 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.1 [578 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf diamond-aligner armhf 0.9.30-3 [475 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.0-13+rpi1 [231 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf liblmdb0 armhf 0.9.24-1 [38.7 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libmbedcrypto3 armhf 2.16.5-1 [194 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libmbedx509-0 armhf 2.16.5-1 [100 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libmbedtls12 armhf 2.16.5-1 [126 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf ncbi-blast+ armhf 2.10.1-3 [9302 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12498 files and directories currently installed.)
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W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-13+rpi1 gcc-10_10.2.0-13+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-7 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.2.0-13+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diamond-aligner_0.9.30-3 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.1.0-1+rpi1 g++-10_10.2.0-13+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.2.0-13+rpi1 gcc-10-base_10.2.0-13+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-13+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.35.1-2+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-6+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-3+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.43-1 libcap2-bin_1:2.43-1 libcc1-0_10.2.0-13+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35-2+rpi1 libctf0_2.35.1-2+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.181-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-13+rpi1 libgcc-s1_10.2.0-13+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran5_10.2.0-13+rpi1 libglib2.0-0_2.66.1-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.2.0-13+rpi1 libgpg-error0_1.38-2 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libksba8_1.4.0-2 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.51+dfsg-1 libldap-common_2.4.51+dfsg-1 liblmdb0_0.9.24-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmbedcrypto3_2.16.5-1 libmbedtls12_2.16.5-1 libmbedx509-0_2.16.5-1 libmount1_2.36-3 libmpc3_1.2.0~rc1-1 libmpfr6_4.1.0-3 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.21-2 libpam-cap_1:2.43-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.6-1 libpython3.8-stdlib_3.8.6-1 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.2-1+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtool_2.4.6-14 libubsan1_10.2.0-13+rpi1 libuchardet0_0.0.7-1 libudev1_246.2-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.36-3 ncbi-blast+_2.10.1-3 ncbi-data_6.1.20170106+dfsg1-9 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 procps_2:3.3.16-5 python3_3.8.2-3 python3-minimal_3.8.2-3 python3.8_3.8.6-1 python3.8-minimal_3.8.6-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-proteinortho-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-4 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.nauCuQB8/trustedkeys.kbx': General error
gpgv: Signature made Tue Oct 20 22:02:43 2020 UTC
gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv:                issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./proteinortho_6.0.24+dfsg-1.dsc
dpkg-source: info: extracting proteinortho in /<<BUILDDIR>>/proteinortho-6.0.24+dfsg
dpkg-source: info: unpacking proteinortho_6.0.24+dfsg.orig.tar.xz
dpkg-source: info: unpacking proteinortho_6.0.24+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying deb_diamond

Check disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-943a8276-11d0-40e2-8984-7845dbb6026c
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

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

dpkg-buildpackage: info: source package proteinortho
dpkg-buildpackage: info: source version 6.0.24+dfsg-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   dh_auto_clean
	make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
rm -rf src/BUILD test/C.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.*
rm -rf src/lapack-3.8.0/
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   dh_auto_build -a
	make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
Creating build directory ...
[ 10%] Prepare proteinortho_clustering ...
[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)
g++ -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -march=native -mtune=native -o src/BUILD/Linux_armv8l/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now  -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
[ 25%] Building **graphMinusRemovegraph**
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_armv8l/proteinortho_graphMinusRemovegraph src/graphMinusRemovegraph.cpp -Wl,-z,relro -Wl,-z,now 
[ 50%] Building **cleanupblastgraph**
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_armv8l/proteinortho_cleanupblastgraph src/cleanupblastgraph.cpp -Wl,-z,relro -Wl,-z,now 
[ 75%] Building **po_tree**
cc -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/proteinortho-6.0.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_armv8l/proteinortho_treeBuilderCore src/po_tree.c -Wl,-z,relro -Wl,-z,now 
src/po_tree.c: In function 'fetch_matrix':
src/po_tree.c:330:2: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
  330 |  fscanf (datei, "%d\n", viecher);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/po_tree.c:341:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
  341 |    fscanf (datei, "%s ",(*pnamen)[i]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/po_tree.c:345:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
  345 |    fscanf (datei, "%s \n",(*pnamen)[i]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/po_tree.c:378:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
  378 |    fscanf (datei, "%c ",&(matrix[i][*ccs]));
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/po_tree.c:381:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
  381 |   fscanf (datei, "%c \n",&(matrix[(*viecher)-1][*ccs]));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Distance = int; _Tp = ConnectedComponent; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
 1819 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
                 from src/proteinortho_clustering.cpp:24:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ConnectedComponent&}; _Tp = ConnectedComponent; _Alloc = std::allocator<ConnectedComponent>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ConnectedComponent>::iterator' changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
  339 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
                 from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_ConnectedComponents>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
 1666 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from src/proteinortho_clustering.cpp:24:
/usr/include/c++/10/bits/stl_vector.h: In function 'void partition_graph()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from src/proteinortho_clustering.cpp:22:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConnectedComponent*, std::vector<ConnectedComponent> >' changed in GCC 7.1
 1891 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
- test max_of_diag() : 1
- test generate_random_vector() : 1
- test get_new_x() : 1
- test makeOrthogonal() : 1
- test normalize() : 1
- test getY() : 1
- test splitGroups() : 1
All test passed.
......OK dynamic linking was successful for proteinortho_clustering!
[100%] Everything is compiled with no errors.
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
   dh_auto_test -a
	make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
[TEST] Clean up all test files...
[TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped)
[TEST] Clean up all test files...
 [1/12] -p=blastp test: passed
 [2/12] -p=blastp+ synteny (PoFF) test: tput: No value for $TERM and no -T specified

tput: No value for $TERM and no -T specified

tput: No value for $TERM and no -T specified

tput: No value for $TERM and no -T specified

passed
 [3/12] -p=diamond test: 
Parameter-vector : (version=6.0.24,step=0,verbose=0,debug=1,exactstep3=0,synteny=0,duplication=2,cs=3,alpha=0.5,connectivity=0.1,cpus=8,evalue=1e-05,purity=1e-07,coverage=50,identity=25,blastmode=diamond,sim=0.95,report=3,keep=0,force=1,selfblast=0,twilight=0,singles=0,clean=0,blastOptions=,nograph=0,xml=0,desc=0,tmp_path=./proteinortho_cache_test_diamond/,blastversion=unknown,binpath=,makedb=diamond makedb --in,blast=,jobs_todo=10,project=test_diamond,po_path=.//src/BUILD/Linux_armv8l,run_id=,threads_per_process=1,useMcl=0,freemem=-1)


[Error]  diamond failed with code 34560. (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)
The most common sources of this error are:
- no space left on device error.
- outdated diamond, please update diamond or consider another -p algorithm.
- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'
- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for diamond? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.  

If you cannot solve this error, please send a report to incoming+paulklemm-phd-proteinortho-7278443-issue-@incoming.gitlab.com including the parameter-vector above or visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes for more help.
Further more all mails to lechner@staff.uni-marburg.de are welcome


Perl exited with active threads:
	7 running and unjoined
	0 finished and unjoined
	0 running and detached
Error, could not open file test_diamond.proteinortho.tsv: No such file or directory at ./src/chk_test.pl line 6.
make[1]: *** [Makefile:266: test_step2] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-6.0.24+dfsg'
dh_auto_test: error: make -j4 test returned exit code 2
make: *** [debian/rules:10: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-10-23T03:49:51Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 6400
Build-Time: 122
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 455
Job: proteinortho_6.0.24+dfsg-1
Machine Architecture: armhf
Package: proteinortho
Package-Time: 595
Source-Version: 6.0.24+dfsg-1
Space: 6400
Status: attempted
Version: 6.0.24+dfsg-1
--------------------------------------------------------------------------------
Finished at 2020-10-23T03:49:51Z
Build needed 00:09:55, 6400k disk space