sbuild (Debian sbuild) 0.91.5 (17 December 2025) on carme.larted.org.uk

+==============================================================================+
| bioperl-run 1.7.3-14 (amd64)                 Tue, 10 Mar 2026 05:01:51 +0000 |
+==============================================================================+

Package: bioperl-run
Version: 1.7.3-14
Source Version: 1.7.3-14
Distribution: perl-5.42-throwaway
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: full

I: Setting up the chroot...
I: Creating chroot session...
I: Setting up log color...

+------------------------------------------------------------------------------+
| Chroot Setup Commands                        Tue, 10 Mar 2026 05:01:51 +0000 |
+------------------------------------------------------------------------------+


/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bioperl-run_1.7.3-14 perl-5.42-throwaway amd64
---------------------------------------------------------------------------------------------------------------------


I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bioperl-run_1.7.3-14 perl-5.42-throwaway amd64'.

Finished processing commands.
--------------------------------------------------------------------------------
I: Setting up apt archive...

+------------------------------------------------------------------------------+
| Update chroot                                Tue, 10 Mar 2026 05:01:52 +0000 |
+------------------------------------------------------------------------------+

Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B]
Hit:2 http://deb.debian.org/debian unstable InRelease
Hit:3 http://deb.debian.org/debian sid InRelease
Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B]
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

+------------------------------------------------------------------------------+
| Fetch source files                           Tue, 10 Mar 2026 05:01:53 +0000 |
+------------------------------------------------------------------------------+


Local sources
-------------

/srv/debomatic/incoming/bioperl-run_1.7.3-14.dsc exists in /srv/debomatic/incoming; copying to chroot

+------------------------------------------------------------------------------+
| Install package build dependencies           Tue, 10 Mar 2026 05:01:54 +0000 |
+------------------------------------------------------------------------------+


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

Merged Build-Depends: debhelper-compat (= 13), libmodule-build-perl, build-essential, perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, libbio-perl-perl, clustalw, emboss, exonerate, hmmer, hyphy-pt | hyphy-mpi, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, libwww-perl
Filtered Build-Depends: debhelper-compat (= 13), libmodule-build-perl, build-essential, perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, libbio-perl-perl, clustalw, emboss, exonerate, hmmer, hyphy-pt, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, libwww-perl
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ InRelease
Get:2 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ Release [615 B]
Ign:3 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ Release.gpg
Get:4 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ Sources [1534 B]
Get:5 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ Packages [1313 B]
Fetched 3462 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Solving dependencies...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 sbuild-build-depends-main-dummy : Depends: debhelper-compat (= 13)
                                   Depends: libmodule-build-perl but it is not going to be installed
                                   Depends: bioperl (>= 1.7.4) but it is not going to be installed
                                   Depends: libalgorithm-diff-perl but it is not going to be installed
                                   Depends: libipc-run-perl but it is not going to be installed
                                   Depends: libio-string-perl but it is not going to be installed
                                   Depends: libxml-twig-perl but it is not going to be installed
                                   Depends: libfile-sort-perl but it is not going to be installed
                                   Depends: libtest-most-perl but it is not going to be installed
                                   Depends: libarray-compare-perl but it is not going to be installed
                                   Depends: libtree-dagnode-perl but it is not going to be installed
                                   Depends: libbio-cluster-perl but it is not going to be installed
                                   Depends: libbio-featureio-perl but it is not going to be installed
                                   Depends: libconfig-any-perl but it is not going to be installed
                                   Depends: libbio-tools-run-alignment-clustalw-perl but it is not going to be installed
                                   Depends: libbio-eutilities-perl but it is not going to be installed
                                   Depends: libbio-tools-run-remoteblast-perl but it is not going to be installed
                                   Depends: amap-align but it is not going to be installed
                                   Depends: bedtools but it is not going to be installed
                                   Depends: bedtools-test but it is not going to be installed
                                   Depends: ncbi-blast+-legacy but it is not going to be installed
                                   Depends: libbio-perl-perl but it is not going to be installed
                                   Depends: clustalw but it is not going to be installed
                                   Depends: emboss but it is not going to be installed
                                   Depends: exonerate but it is not going to be installed
                                   Depends: hmmer but it is not going to be installed
                                   Depends: hyphy-pt but it is not going to be installed
                                   Depends: infernal but it is not going to be installed
                                   Depends: kalign but it is not going to be installed
                                   Depends: mafft but it is not going to be installed
                                   Depends: muscle but it is not going to be installed
                                   Depends: ncoils but it is not going to be installed
                                   Depends: phyml but it is not going to be installed
                                   Depends: primer3 but it is not going to be installed
                                   Depends: probcons but it is not going to be installed
                                   Depends: python3-pybedtools but it is not going to be installed
                                   Depends: raxml but it is not going to be installed
                                   Depends: samtools but it is not going to be installed
                                   Depends: sim4 but it is not going to be installed
                                   Depends: tigr-glimmer but it is not going to be installed
                                   Depends: wise but it is not going to be installed
                                   Depends: fasttree but it is not going to be installed
E: Unable to satisfy dependencies. Reached two conflicting assignments:
   1. libclone-perl:amd64=0.48-1 is selected for install because:
      1. sbuild-build-depends-main-dummy:amd64=0.invalid.0 is selected for install
      2. sbuild-build-depends-main-dummy:amd64 Depends libbio-eutilities-perl
      3. libbio-eutilities-perl:amd64 Depends libhttp-message-perl
      4. libhttp-message-perl:amd64 Depends libclone-perl
      5. libclone-perl:amd64 is available in versions 0.48-1, 0.47-1+b3
         [selected libclone-perl:amd64]
      For context, additional choices that could not be installed:
      * In libclone-perl:amd64 is available in versions 0.48-1, 0.47-1+b3:
        - libclone-perl:amd64=0.47-1+b3 is not selected for install
   2. libclone-perl:amd64=0.48-1 Depends perlapi-5.40.1
      but none of the choices are installable:
      - perl-base:amd64=5.40.1-7 is not selected for install
                                   Depends: lagan but it is not going to be installed
                                   Depends: pal2nal but it is not going to be installed
                                   Depends: pftools but it is not going to be installed
                                   Depends: libwww-perl but it is not going to be installed
apt-get failed.
E: Package installation failed
Not removing build depends: cloned chroot in use

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

Merged Build-Depends: dose-distcheck
Filtered Build-Depends: dose-distcheck
dpkg-deb: building package 'sbuild-build-depends-dose3-dummy' in '/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive/sbuild-build-depends-dose3-dummy.deb'.
Ign:1 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ InRelease
Get:2 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ Release [615 B]
Ign:3 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ Release.gpg
Get:4 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ Sources [2113 B]
Get:5 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ Packages [1928 B]
Fetched 4656 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install dose3 build dependencies (apt-based resolver)
-----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Solving dependencies...
The following additional packages will be installed:
  dose-distcheck
The following NEW packages will be installed:
  dose-distcheck sbuild-build-depends-dose3-dummy
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 1265 kB of archives.
After this operation, 5135 kB of additional disk space will be used.
Get:1 copy:/build/bioperl-run-1CmS2M/resolver-Mc6CKW/apt_archive ./ sbuild-build-depends-dose3-dummy 0.invalid.0 [836 B]
Get:2 http://deb.debian.org/debian unstable/main amd64 dose-distcheck amd64 7.0.0-7 [1264 kB]
Fetched 1265 kB in 0s (58.9 MB/s)
Selecting previously unselected package dose-distcheck.
(Reading database ... 23438 files and directories currently installed.)
Preparing to unpack .../dose-distcheck_7.0.0-7_amd64.deb ...
Unpacking dose-distcheck (7.0.0-7) ...
Selecting previously unselected package sbuild-build-depends-dose3-dummy.
Preparing to unpack .../sbuild-build-depends-dose3-dummy_0.invalid.0_amd64.deb ...
Unpacking sbuild-build-depends-dose3-dummy (0.invalid.0) ...
Setting up dose-distcheck (7.0.0-7) ...
Setting up sbuild-build-depends-dose3-dummy (0.invalid.0) ...
(I)Doseparse: Parsing and normalizing...
(I)Dose_deb: Parsing Packages file -...
(I)Dose_common: total packages 76577
(I)Dose_applications: Cudf Universe: 76577 packages
(I)Dose_applications: --checkonly specified, consider all packages as background packages
(I)Dose_applications: Solving...
output-version: 1.2
native-architecture: amd64
report:
 -
  package: sbuild-build-depends-main-dummy
  version: 0.invalid.0
  architecture: amd64
  status: ok
  installationset:
   -
    package: zlib1g
    version: 1:1.3.dfsg+really1.3.1-3
    architecture: amd64
   -
    package: xz-utils
    version: 5.8.2-2
    architecture: amd64
   -
    package: wise-data
    version: 2.4.1-28
    architecture: all
   -
    package: wise
    version: 2.4.1-28
    architecture: amd64
   -
    package: util-linux
    version: 2.41.3-4
    architecture: amd64
    essential: true
   -
    package: ucf
    version: 3.0052
    architecture: all
   -
    package: tzdata
    version: 2026a-1
    architecture: all
   -
    package: tigr-glimmer
    version: 3.02b-6+b1
    architecture: amd64
   -
    package: tar
    version: 1.35+dfsg-4
    architecture: amd64
    essential: true
   -
    package: sysvinit-utils
    version: 3.15-6
    architecture: amd64
    essential: true
   -
    package: sse4.2-support
    version: 27+b1
    architecture: amd64
   -
    package: sim4
    version: 0.0.20121010-9
    architecture: amd64
   -
    package: sensible-utils
    version: 0.0.26
    architecture: all
   -
    package: sed
    version: 4.9-2
    architecture: amd64
    essential: true
   -
    package: sbuild-build-depends-main-dummy
    version: 0.invalid.0
    architecture: amd64
   -
    package: samtools
    version: 1.22.1-1
    architecture: amd64
   -
    package: rpcsvc-proto
    version: 1.4.3-1
    architecture: amd64
   -
    package: readline-common
    version: 8.3-4
    architecture: all
   -
    package: raxml
    version: 8.2.13+dfsg-3
    architecture: amd64
   -
    package: python3.13-minimal
    version: 3.13.12-1
    architecture: amd64
   -
    package: python3.13
    version: 3.13.12-1
    architecture: amd64
   -
    package: python3-pysam
    version: 0.23.3+ds-2+b1
    architecture: amd64
   -
    package: python3-pybedtools
    version: 0.10.0-6
    architecture: amd64
   -
    package: python3-numpy-dev
    version: 1:2.3.5+ds-3
    architecture: amd64
   -
    package: python3-numpy
    version: 1:2.3.5+ds-3
    architecture: amd64
   -
    package: python3-minimal
    version: 3.13.9-3
    architecture: amd64
   -
    package: python3
    version: 3.13.9-3
    architecture: amd64
   -
    package: procps
    version: 2:4.0.4-9+b1
    architecture: amd64
   -
    package: probcons
    version: 1.12-15
    architecture: amd64
   -
    package: primer3
    version: 2.6.1-6
    architecture: amd64
   -
    package: po-debconf
    version: 1.0.22
    architecture: all
   -
    package: phyml
    version: 3:3.3.20250515-2
    architecture: amd64
   -
    package: pftools
    version: 3.2.12-3
    architecture: amd64
   -
    package: perl-openssl-defaults
    version: 7+b2
    architecture: amd64
   -
    package: perl-modules-5.42
    version: 5.42.0-3
    architecture: all
   -
    package: perl-base
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    architecture: amd64
    essential: true
   -
    package: perl
    version: 5.42.0-3
    architecture: amd64
   -
    package: patch
    version: 2.8-2
    architecture: amd64
   -
    package: passwd
    version: 1:4.19.3-1
    architecture: amd64
   -
    package: pal2nal
    version: 14.1-3
    architecture: all
   -
    package: opensysusers
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    architecture: all
   -
    package: openssl-provider-legacy
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    architecture: amd64
   -
    package: openssl
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   -
    package: openssh-client
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    architecture: amd64
   -
    package: openmpi-common
    version: 5.0.10-1
    architecture: all
   -
    package: openmpi-bin
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   -
    package: ocl-icd-libopencl1
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    architecture: amd64
   -
    package: netbase
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   -
    package: ncurses-bin
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    essential: true
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    package: ncurses-base
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   -
    package: ncoils
    version: 2002-10
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   -
    package: ncbi-vdb-data
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    architecture: all
   -
    package: ncbi-data
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    architecture: all
   -
    package: ncbi-blast+-legacy
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    architecture: all
   -
    package: ncbi-blast+
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    architecture: amd64
   -
    package: mysql-common
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    architecture: all
   -
    package: muscle
    version: 1:5.1.0-1
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   -
    package: mpi-default-bin
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    architecture: amd64
   -
    package: media-types
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   -
    package: mariadb-common
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   -
    package: make-guile
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   -
    package: mafft
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   -
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    package: login.defs
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   -
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    package: libxml-writer-perl
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    package: libxml-sax-expat-perl
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   -
    package: libxml-namespacesupport-perl
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   -
    package: libx11-6
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    package: libwww-robotrules-perl
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    package: libwww-perl
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    package: libubsan1
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   -
    package: libtype-tiny-perl
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    package: libtsan2
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   -
    package: libtry-tiny-perl
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    package: libtree-dagnode-perl
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   -
    package: libtimedate-perl
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    package: libtiff6
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   -
    package: libtext-wrapi18n-perl
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    package: libtext-diff-perl
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    package: libtext-csv-perl
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    package: libtext-charwidth-perl
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   -
    package: libtest-warn-perl
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    package: libtest-most-perl
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    package: libtest-exception-perl
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    package: libtest-differences-perl
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    package: libtest-deep-perl
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    package: libtasn1-6
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   -
    package: libsystemd0
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    architecture: amd64
   -
    package: libsvtav1enc2
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    architecture: amd64
   -
    package: libsub-uplevel-perl
    version: 0.2800-3
    architecture: all
   -
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total-packages: 76577
broken-packages: 0

+------------------------------------------------------------------------------+
| Cleanup                                      Tue, 10 Mar 2026 05:02:07 +0000 |
+------------------------------------------------------------------------------+

Purging /build/bioperl-run-1CmS2M
Not cleaning session: cloned chroot in use
E: Package build dependencies not satisfied; skipping

+------------------------------------------------------------------------------+
| Summary                                      Tue, 10 Mar 2026 05:02:08 +0000 |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: full
Build-Space: n/a
Build-Time: 0
Distribution: perl-5.42-throwaway
Fail-Stage: install-deps
Host Architecture: amd64
Install-Time: 0
Job: /srv/debomatic/incoming/bioperl-run_1.7.3-14.dsc
Machine Architecture: amd64
Package: bioperl-run
Package-Time: 0
Source-Version: 1.7.3-14
Space: n/a
Status: given-back
Version: 1.7.3-14
--------------------------------------------------------------------------------
Finished at 2026-03-10T05:01:51Z
Build needed 00:00:00, no disk space