Your message dated Mon, 09 Mar 2026 21:07:16 +0000
with message-id <[email protected]>
and subject line Bug#1129866: fixed in bioperl-run 1.7.3-14
has caused the Debian Bug report #1129866,
regarding bioperl-run: FTBFS: Failed 1/60 test programs. 1/1650 subtests failed.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1129866: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1129866
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:bioperl-run
Version: 1.7.3-13
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202603/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:bioperl-run, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --install_scripts
/usr/bin/perl Build.PL --installdirs vendor --config optimize="-g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2"
--config ld="x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wl,-z,relro" --install_scripts
Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n ]n
Can't find dist packages without a MANIFEST file
Run 'Build manifest' to generate one
[... snipped ...]
ok 62 - bl2seq (blastx)
ok 63 - got hit
ok 64 - bl2seq (blastp)
ok 65 - no hit
ok 66 - bl2seq (blastp)
ok 67 - got hit
ok 68 - bl2seq (tblastx) - multiple outfmt options
ok 69 - bl2seq (tblastx) - multiple outfmt options (use method arg)
ok 70 - bl2seq (tblastx) - multiple outfmt options (no explict quotes should
also work)
ok 71 - bl2seq (tblastx) - multiple outfmt options (a single format number in
quotes
ok
# Required executable for Bio::Tools::Run::Phylo::SLR is not present
t/SLR.t .......................
1..7
ok 1 - use Bio::Root::IO;
ok 2 - use Bio::Tools::Run::Phylo::SLR;
ok 3 - use Bio::AlignIO;
ok 4 - use Bio::TreeIO;
ok 5
ok 6 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present
ok 7 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present
ok
t/Samtools.t ..................
1..41
ok 1 - make a factory using command 'pileup'
ok 2 - parameters changed on construction
ok 3 - access parameter
ok 4 - parameters_changed cleared on read
ok 5 - set a param not set in constructor
ok 6 - parameters_changed set
ok 7 - parameter really set
ok 8 - original parameter unchanged
ok 9 - parameters_changed cleared on read
ok 10 - change an original parameter
ok 11 - parameter really changed
ok 12 - reset parameters with arg
ok 13 - original parameters undefined
ok 14 - parameter really reset via arg
ok 15 - parameters changed
ok 16 - all available options
ok 17 - available parameters
ok 18 - available switches
ok 19 - get_parameters correct
ok 20 - command attribute set
ok 21 - internal command array set
ok 22 - internal prefix hash set
ok 23 - commands filtered by prefix
ok 24 - translate_params: command correct
ok 25 - translate_params: options correct
ok 26 - merge bam factory instantiated
ok 27 - merged bam file created
ok 28 - fasta index factory
ok 29 - make fasta index
ok 30 - fai file present
ok 31 - bam -> sam cvt factory
ok 32 - convert bam -> sam
ok 33 - sam file present and text
ok 34 - sam -> bam cvt factory
ok 35 - convert sam -> bam
ok 36 - bam file present and binary
ok 37 - bam sort factory
ok 38 - sort bam file
ok 39 - bam index factory
ok 40 - make bam index
ok 41 - bai file present and binary
ok
# Required executable for Bio::Tools::Run::Seg is not present
t/Seg.t .......................
1..8
ok 1 - use Bio::Tools::Run::Seg;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Seq;
ok 4 - An object of class 'Bio::Tools::Run::Seg' isa 'Bio::Tools::Run::Seg'
ok 5 # skip Required executable for Bio::Tools::Run::Seg is not present
ok 6 # skip Required executable for Bio::Tools::Run::Seg is not present
ok 7 # skip Required executable for Bio::Tools::Run::Seg is not present
ok 8 # skip Required executable for Bio::Tools::Run::Seg is not present
ok
# Required executable for Bio::Tools::Run::Phylo::Semphy is not present
t/Semphy.t ....................
1..19
ok 1 - use Bio::Tools::Run::Phylo::Semphy;
ok 2 - An object of class 'Bio::Tools::Run::Phylo::Semphy' isa
'Bio::Tools::Run::Phylo::Semphy'
ok 3 - has a created method not in args
ok 4 - ratio param was set via -z
ok 5 - jtt switch was set
ok 6 - program_dir returned correct default
ok 7 - Correct exe default name
ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not
present
ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present
t/SeqBoot.t ...................
1..9
ok 1 - use Bio::Tools::Run::Phylo::Phylip::SeqBoot;
ok 2 - use Bio::AlignIO;
ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is
not present
ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is
not present
ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is
not present
ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is
not present
ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is
not present
ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is
not present
ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is
not present
ok
# Required executable for Bio::Tools::Run::Signalp is not present
t/Signalp.t ...................
1..7
ok 1 - use Bio::Tools::Run::Signalp;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Seq;
ok 4 - An object of class 'Bio::Tools::Run::Signalp' isa
'Bio::Tools::Run::Signalp'
ok 5 # skip Required executable for Bio::Tools::Run::Signalp is not present
ok 6 # skip Required executable for Bio::Tools::Run::Signalp is not present
ok 7 # skip Required executable for Bio::Tools::Run::Signalp is not present
ok
t/Sim4.t ......................
1..23
ok 1 - use Bio::Tools::Run::Alignment::Sim4;
ok 2 - use Bio::SimpleAlign;
ok 3 - use Bio::AlignIO;
ok 4 - use Bio::SeqIO;
ok 5 - An object of class 'Bio::Tools::Run::Alignment::Sim4' isa
'Bio::Tools::Run::Alignment::Sim4'
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
# Required executable for Bio::Tools::Run::Simprot is not present
t/Simprot.t ...................
1..6
ok 1 - use Bio::Root::IO;
ok 2 - use Bio::Tools::Run::Simprot;
ok 3 - use Bio::AlignIO;
ok 4 - use Bio::TreeIO;
ok 5
ok 6 # skip Required executable for Bio::Tools::Run::Simprot is not present
ok
t/SoapEU-function.t ........... skipped: The optional module Bio::DB::ESoap (or
dependencies thereof) was not installed
t/SoapEU-unit.t ............... skipped: The optional module Bio::DB::ESoap (or
dependencies thereof) was not installed
# Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not
present
t/StandAloneFasta.t ...........
1..15
ok 1 - use Bio::Tools::Run::Alignment::StandAloneFasta;
ok 2 - use Bio::SeqIO;
ok 3
ok 4 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta
is not present
ok 5 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta
is not present
ok 6 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta
is not present
ok 7 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta
is not present
ok 8 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta
is not present
ok 9 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta
is not present
ok 10 # skip Required executable for
Bio::Tools::Run::Alignment::StandAloneFasta is not present
ok 11 # skip Required executable for
Bio::Tools::Run::Alignment::StandAloneFasta is not present
ok 12 # skip Required executable for
Bio::Tools::Run::Alignment::StandAloneFasta is not present
ok 13 # skip Required executable for
Bio::Tools::Run::Alignment::StandAloneFasta is not present
ok 14 # skip Required executable for
Bio::Tools::Run::Alignment::StandAloneFasta is not present
ok 15 # skip Required executable for
Bio::Tools::Run::Alignment::StandAloneFasta is not present
ok
# Required executable for Bio::Tools::Run::Tmhmm is not present
t/Tmhmm.t .....................
1..9
ok 1 - use Bio::Tools::Run::Tmhmm;
ok 2 - use Bio::SeqIO;
ok 3 - An object of class 'Bio::Tools::Run::Tmhmm' isa 'Bio::Tools::Run::Tmhmm'
ok 4 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
ok 5 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
ok 6 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
ok 7 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
ok 8 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
ok 9 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
ok
t/TribeMCL.t ..................
1..24
ok 1 - use Bio::Tools::Run::TribeMCL;
ok 2 - use Bio::SearchIO;
ok 3 - An object of class 'Bio::Tools::Run::TribeMCL' isa
'Bio::Tools::Run::TribeMCL'
ok 4 # skip Tribe Matrix program not found. Skipping tests...
ok 5 # skip Tribe Matrix program not found. Skipping tests...
ok 6 # skip Tribe Matrix program not found. Skipping tests...
ok 7 # skip Tribe Matrix program not found. Skipping tests...
ok 8 # skip Tribe Matrix program not found. Skipping tests...
ok 9 # skip Tribe Matrix program not found. Skipping tests...
ok 10 # skip Tribe Matrix program not found. Skipping tests...
ok 11 # skip Tribe Matrix program not found. Skipping tests...
ok 12 # skip Tribe Matrix program not found. Skipping tests...
ok 13 # skip Tribe Matrix program not found. Skipping tests...
ok 14 # skip Tribe Matrix program not found. Skipping tests...
ok 15 # skip Tribe Matrix program not found. Skipping tests...
ok 16 # skip Tribe Matrix program not found. Skipping tests...
ok 17 # skip Tribe Matrix program not found. Skipping tests...
ok 18 # skip Tribe Matrix program not found. Skipping tests...
ok 19 # skip Tribe Matrix program not found. Skipping tests...
ok 20 # skip Tribe Matrix program not found. Skipping tests...
ok 21 # skip Tribe Matrix program not found. Skipping tests...
ok 22 # skip Tribe Matrix program not found. Skipping tests...
ok 23 # skip Tribe Matrix program not found. Skipping tests...
ok 24 # skip Tribe Matrix program not found. Skipping tests...
ok
t/Vista.t .....................
1..7
ok 1 - use Bio::Tools::Run::Vista;
ok 2 - use Bio::AlignIO;
ok 3 # skip Skipping due to old java version
ok 4 # skip Skipping due to old java version
ok 5 # skip Skipping due to old java version
ok 6 # skip Skipping due to old java version
ok 7 # skip Skipping due to old java version
ok
# Required executable for Bio::Tools::Run::Alignment::Gmap is not present
t/gmap-run.t ..................
1..8
ok 1 - use Bio::Tools::Run::Alignment::Gmap;
ok 2 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not
present
ok 3 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not
present
ok 4 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not
present
ok 5 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not
present
ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not
present
ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not
present
ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not
present
ok
# Required executable for Bio::Tools::Run::tRNAscanSE is not present
t/tRNAscanSE.t ................
1..12
ok 1 - use Bio::Tools::Run::tRNAscanSE;
ok 2 - use Bio::Root::IO;
ok 3 - use Bio::Seq;
ok 4 - An object of class 'Bio::Tools::Run::tRNAscanSE' isa
'Bio::Tools::Run::tRNAscanSE'
ok 5 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
ok 6 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
ok 7 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
ok 8 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
ok
Test Summary Report
-------------------
t/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0)
TODO passed: 20, 57, 75, 88, 110, 155, 190, 208, 226
262, 280, 315, 333, 405
t/Kalign.t (Wstat: 6400 (exited 25) Tests: 5 Failed: 1)
Failed test: 5
Non-zero exit status: 25
Parse errors: Bad plan. You planned 7 tests but ran 5.
Files=60, Tests=1650, 103 wallclock secs ( 0.15 usr 0.09 sys + 95.56 cusr
8.07 csys = 103.87 CPU)
Result: FAIL
Failed 1/60 test programs. 1/1650 subtests failed.
dh_auto_test: error: /usr/bin/perl Build test --verbose 1 returned exit code 255
make[1]: *** [debian/rules:37: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:28: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: bioperl-run
Source-Version: 1.7.3-14
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
bioperl-run, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated bioperl-run package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 09 Mar 2026 20:43:42 +0100
Source: bioperl-run
Architecture: source
Version: 1.7.3-14
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1129866
Changes:
bioperl-run (1.7.3-14) unstable; urgency=medium
.
* update-kalign-invocation.patch: new.
This change adjusts arguments passed to kalign to use stdin as input
and stdout as output, per the new command version's usage
instructions. (Closes: #1129866)
* d/control: drop redundant Priority: optional.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.3.
* d/watch: rework to port to Github uscan template.
Checksums-Sha1:
fd4e2f69ed7578e5735d0b54ad228edbed369a8c 3217 bioperl-run_1.7.3-14.dsc
5741908702debfb2b787916a18159a5ceeddec2d 20384
bioperl-run_1.7.3-14.debian.tar.xz
Checksums-Sha256:
d5ed6988808775823202f960b09ba6f37abe0c7e5e7d29dd57a5a1d489c333af 3217
bioperl-run_1.7.3-14.dsc
5176f6e8d38e77234ba1dd09ca5979dd76b7c08cef3407f7a4f856217a534c89 20384
bioperl-run_1.7.3-14.debian.tar.xz
Files:
8e322cd8462beb3d20f8a8d75294ad27 3217 science optional bioperl-run_1.7.3-14.dsc
fb6ed77cf4d5a9e91e5b82cc8e55793a 20384 science optional
bioperl-run_1.7.3-14.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=31pO
-----END PGP SIGNATURE-----
pgpxSDTaY9_9a.pgp
Description: PGP signature
--- End Message ---
