Bug#925909: pbgenomicconsensus: autopkgtest regression

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Bug#925909: pbgenomicconsensus: autopkgtest regression

Graham Inggs-3
Source: pbgenomicconsensus
Version: 2.3.2-1
Severity: serious
X-Debbugs-CC: [hidden email]
User: [hidden email]
Usertags: regression

Hi Maintainer

Since the upload of 2.3.2-1, pbgenomicconsensus has been failing its own
autopkgtests [1] with the following error:

autopkgtest [12:23:51]: test command2: [-----------------------
# Tests that need to be run by Jenkins but are slowing
# down the development cycle, so aren't run by "tests"
# target.
PATH=`pwd`:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games cram
--verbose --xunit-file=gc-extra-cram.xml `ls tests/cram/extra/*.t | grep
-v arrow`
tests/cram/extra/plurality-fluidigm.t: failed
--- tests/cram/extra/plurality-fluidigm.t
+++ tests/cram/extra/plurality-fluidigm.t.err
@@ -8,12 +8,26 @@
  Set the QV threshold to 10.

    $ variantCaller --algorithm=plurality -r $REFERENCE -q 10 -o
variants.gff -o consensus.csv -o consensus.fastq $INPUT
+  Traceback (most recent call last):
+    File "/usr/bin/variantCaller", line 3, in <module>
+      from GenomicConsensus.main import main
+    File "/usr/lib/python2.7/dist-packages/GenomicConsensus/main.py",
line 16, in <module>
+      from GenomicConsensus import reference
+    File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/reference.py", line
8, in <module>
+      from .windows import holes, kCoveredIntervals, enumerateIntervals
+    File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/windows.py", line 14,
in <module>
+      from ConsensusCore import CoveredIntervals
+  ImportError: No module named ConsensusCore
+  [1]

  There are two true SNVs (and one diploid SNV that we miss right now).

    $ grep insertion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep deletion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep substitution variants.gff
-
EGFR_Exon_23\t.\tsubstitution\t48\t48\t.\t.\t.\treference=T;variantSeq=C;frequency=97;coverage=100;confidence=40
(esc)
+  grep: variants.gff: No such file or directory
+  [2]
# Ran 1 tests, 0 skipped, 1 failed.
make: *** [Makefile:25: extra-tests] Error 1
autopkgtest [12:23:52]: test command2: -----------------------]
autopkgtest [12:23:52]: test command2:  - - - - - - - - - - results - -
- - - - - - - -
command2             FAIL non-zero exit status 2

Regards
Graham


[1] https://ci.debian.net/packages/p/pbgenomicconsensus/unstable/amd64/

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Bug#925909: pbgenomicconsensus: autopkgtest regression

Andreas Tille-2
Control: tags -1 pending

Hi,

I commited some changes to Git which are not sufficient yet but
I think I have a clue I can implement in the next 2-3 days.

Thanks for spotting this issue

      Andreas.

--
http://fam-tille.de

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Processed: Re: Bug#925909: pbgenomicconsensus: autopkgtest regression

Debian Bug Tracking System
In reply to this post by Graham Inggs-3
Processing control commands:

> tags -1 pending
Bug #925909 [src:pbgenomicconsensus] pbgenomicconsensus: autopkgtest regression
Added tag(s) pending.

--
925909: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925909
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Bug#925909: marked as done (pbgenomicconsensus: autopkgtest regression)

Debian Bug Tracking System
In reply to this post by Graham Inggs-3
Your message dated Tue, 02 Apr 2019 09:35:23 +0000
with message-id <[hidden email]>
and subject line Bug#925909: fixed in pbgenomicconsensus 2.3.2-2
has caused the Debian Bug report #925909,
regarding pbgenomicconsensus: autopkgtest regression
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 [hidden email]
immediately.)


--
925909: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925909
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Contact [hidden email] with problems

Source: pbgenomicconsensus
Version: 2.3.2-1
Severity: serious
X-Debbugs-CC: [hidden email]
User: [hidden email]
Usertags: regression

Hi Maintainer

Since the upload of 2.3.2-1, pbgenomicconsensus has been failing its own
autopkgtests [1] with the following error:

autopkgtest [12:23:51]: test command2: [-----------------------
# Tests that need to be run by Jenkins but are slowing
# down the development cycle, so aren't run by "tests"
# target.
PATH=`pwd`:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games cram
--verbose --xunit-file=gc-extra-cram.xml `ls tests/cram/extra/*.t | grep
-v arrow`
tests/cram/extra/plurality-fluidigm.t: failed
--- tests/cram/extra/plurality-fluidigm.t
+++ tests/cram/extra/plurality-fluidigm.t.err
@@ -8,12 +8,26 @@
  Set the QV threshold to 10.

    $ variantCaller --algorithm=plurality -r $REFERENCE -q 10 -o
variants.gff -o consensus.csv -o consensus.fastq $INPUT
+  Traceback (most recent call last):
+    File "/usr/bin/variantCaller", line 3, in <module>
+      from GenomicConsensus.main import main
+    File "/usr/lib/python2.7/dist-packages/GenomicConsensus/main.py",
line 16, in <module>
+      from GenomicConsensus import reference
+    File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/reference.py", line
8, in <module>
+      from .windows import holes, kCoveredIntervals, enumerateIntervals
+    File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/windows.py", line 14,
in <module>
+      from ConsensusCore import CoveredIntervals
+  ImportError: No module named ConsensusCore
+  [1]

  There are two true SNVs (and one diploid SNV that we miss right now).

    $ grep insertion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep deletion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep substitution variants.gff
-
EGFR_Exon_23\t.\tsubstitution\t48\t48\t.\t.\t.\treference=T;variantSeq=C;frequency=97;coverage=100;confidence=40
(esc)
+  grep: variants.gff: No such file or directory
+  [2]
# Ran 1 tests, 0 skipped, 1 failed.
make: *** [Makefile:25: extra-tests] Error 1
autopkgtest [12:23:52]: test command2: -----------------------]
autopkgtest [12:23:52]: test command2:  - - - - - - - - - - results - -
- - - - - - - -
command2             FAIL non-zero exit status 2

Regards
Graham


[1] https://ci.debian.net/packages/p/pbgenomicconsensus/unstable/amd64/

Source: pbgenomicconsensus
Source-Version: 2.3.2-2

We believe that the bug you reported is fixed in the latest version of
pbgenomicconsensus, 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 [hidden email],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <[hidden email]> (supplier of updated pbgenomicconsensus 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 [hidden email])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Tue, 02 Apr 2019 11:02:18 +0200
Source: pbgenomicconsensus
Binary: pbgenomicconsensus python-pbgenomicconsensus
Architecture: source
Version: 2.3.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <[hidden email]>
Changed-By: Andreas Tille <[hidden email]>
Description:
 pbgenomicconsensus - Pacific Biosciences variant and consensus caller
 python-pbgenomicconsensus - Pacific Biosciences variant and consensus caller (Python 2)
Closes: 925909
Changes:
 pbgenomicconsensus (2.3.2-2) unstable; urgency=medium
 .
   [ Afif Elghraoui ]
   * Remove myself from Uploaders
 .
   [ Andreas Tille ]
   * Add myself to Uploaders
   * python-pbgenomicconsensus Depends: python-pbconsensuscore
   * Test Depends: poa
   * Ignore some warnings which are breaking test results, remove
     tests that are based on non-existing input data
   * Move exclusion of tests to upstream Makefile via patch rather than
     in d/rules.  This is needed to run autopkgtest successfully
     Closes: #925909
Checksums-Sha1:
 9f41882f3e8313171b61ab02968c3b7b391b23c6 2491 pbgenomicconsensus_2.3.2-2.dsc
 bc0fbc911ba3d14cee8bb6b602bf2e3b139277f2 20656 pbgenomicconsensus_2.3.2-2.debian.tar.xz
Checksums-Sha256:
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Files:
 0dbe343ccf0f533b63f8c80bdeb5884b 2491 science optional pbgenomicconsensus_2.3.2-2.dsc
 cd25a77bf24040e8b153a921df171769 20656 science optional pbgenomicconsensus_2.3.2-2.debian.tar.xz

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Bug#925909: marked as done (pbgenomicconsensus: autopkgtest regression)

Debian Bug Tracking System
In reply to this post by Graham Inggs-3
Your message dated Sat, 06 Apr 2019 10:18:35 +0000
with message-id <[hidden email]>
and subject line Bug#925909: fixed in pbgenomicconsensus 2.3.2-4
has caused the Debian Bug report #925909,
regarding pbgenomicconsensus: autopkgtest regression
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 [hidden email]
immediately.)


--
925909: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925909
Debian Bug Tracking System
Contact [hidden email] with problems

Source: pbgenomicconsensus
Version: 2.3.2-1
Severity: serious
X-Debbugs-CC: [hidden email]
User: [hidden email]
Usertags: regression

Hi Maintainer

Since the upload of 2.3.2-1, pbgenomicconsensus has been failing its own
autopkgtests [1] with the following error:

autopkgtest [12:23:51]: test command2: [-----------------------
# Tests that need to be run by Jenkins but are slowing
# down the development cycle, so aren't run by "tests"
# target.
PATH=`pwd`:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games cram
--verbose --xunit-file=gc-extra-cram.xml `ls tests/cram/extra/*.t | grep
-v arrow`
tests/cram/extra/plurality-fluidigm.t: failed
--- tests/cram/extra/plurality-fluidigm.t
+++ tests/cram/extra/plurality-fluidigm.t.err
@@ -8,12 +8,26 @@
  Set the QV threshold to 10.

    $ variantCaller --algorithm=plurality -r $REFERENCE -q 10 -o
variants.gff -o consensus.csv -o consensus.fastq $INPUT
+  Traceback (most recent call last):
+    File "/usr/bin/variantCaller", line 3, in <module>
+      from GenomicConsensus.main import main
+    File "/usr/lib/python2.7/dist-packages/GenomicConsensus/main.py",
line 16, in <module>
+      from GenomicConsensus import reference
+    File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/reference.py", line
8, in <module>
+      from .windows import holes, kCoveredIntervals, enumerateIntervals
+    File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/windows.py", line 14,
in <module>
+      from ConsensusCore import CoveredIntervals
+  ImportError: No module named ConsensusCore
+  [1]

  There are two true SNVs (and one diploid SNV that we miss right now).

    $ grep insertion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep deletion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep substitution variants.gff
-
EGFR_Exon_23\t.\tsubstitution\t48\t48\t.\t.\t.\treference=T;variantSeq=C;frequency=97;coverage=100;confidence=40
(esc)
+  grep: variants.gff: No such file or directory
+  [2]
# Ran 1 tests, 0 skipped, 1 failed.
make: *** [Makefile:25: extra-tests] Error 1
autopkgtest [12:23:52]: test command2: -----------------------]
autopkgtest [12:23:52]: test command2:  - - - - - - - - - - results - -
- - - - - - - -
command2             FAIL non-zero exit status 2

Regards
Graham


[1] https://ci.debian.net/packages/p/pbgenomicconsensus/unstable/amd64/

Source: pbgenomicconsensus
Source-Version: 2.3.2-4

We believe that the bug you reported is fixed in the latest version of
pbgenomicconsensus, 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 [hidden email],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <[hidden email]> (supplier of updated pbgenomicconsensus 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 [hidden email])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Sat, 06 Apr 2019 11:16:49 +0200
Source: pbgenomicconsensus
Architecture: source
Version: 2.3.2-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <[hidden email]>
Changed-By: Andreas Tille <[hidden email]>
Closes: 925909
Changes:
 pbgenomicconsensus (2.3.2-4) unstable; urgency=medium
 .
   * Fix dependencies
     Closes: #925909
   * unset GZIP in autopkgtest
Checksums-Sha1:
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 f43bc2527928c224bf07f891030190b95aafcd0402df09d3cfed9a40d20c6bc3 20716 pbgenomicconsensus_2.3.2-4.debian.tar.xz
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Files:
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 4cea3a8d9c32862eb466b249ae620c9b 20716 science optional pbgenomicconsensus_2.3.2-4.debian.tar.xz
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Processed: [Help] Re: pbgenomicconsensus: autopkgtest regression

Debian Bug Tracking System
In reply to this post by Graham Inggs-3
Processing control commands:

> reopen -1
Bug #925909 {Done: Andreas Tille <[hidden email]>} [src:pbgenomicconsensus] pbgenomicconsensus: autopkgtest regression
'reopen' may be inappropriate when a bug has been closed with a version;
all fixed versions will be cleared, and you may need to re-add them.
Bug reopened
No longer marked as fixed in versions pbgenomicconsensus/2.3.2-4.

--
925909: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925909
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Contact [hidden email] with problems

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Bug#925909: marked as done (pbgenomicconsensus: autopkgtest regression)

Debian Bug Tracking System
In reply to this post by Graham Inggs-3
Your message dated Sun, 07 Apr 2019 15:33:36 +0000
with message-id <[hidden email]>
and subject line Bug#925909: fixed in pbgenomicconsensus 2.3.2-5
has caused the Debian Bug report #925909,
regarding pbgenomicconsensus: autopkgtest regression
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 [hidden email]
immediately.)


--
925909: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925909
Debian Bug Tracking System
Contact [hidden email] with problems

Source: pbgenomicconsensus
Version: 2.3.2-1
Severity: serious
X-Debbugs-CC: [hidden email]
User: [hidden email]
Usertags: regression

Hi Maintainer

Since the upload of 2.3.2-1, pbgenomicconsensus has been failing its own
autopkgtests [1] with the following error:

autopkgtest [12:23:51]: test command2: [-----------------------
# Tests that need to be run by Jenkins but are slowing
# down the development cycle, so aren't run by "tests"
# target.
PATH=`pwd`:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games cram
--verbose --xunit-file=gc-extra-cram.xml `ls tests/cram/extra/*.t | grep
-v arrow`
tests/cram/extra/plurality-fluidigm.t: failed
--- tests/cram/extra/plurality-fluidigm.t
+++ tests/cram/extra/plurality-fluidigm.t.err
@@ -8,12 +8,26 @@
  Set the QV threshold to 10.

    $ variantCaller --algorithm=plurality -r $REFERENCE -q 10 -o
variants.gff -o consensus.csv -o consensus.fastq $INPUT
+  Traceback (most recent call last):
+    File "/usr/bin/variantCaller", line 3, in <module>
+      from GenomicConsensus.main import main
+    File "/usr/lib/python2.7/dist-packages/GenomicConsensus/main.py",
line 16, in <module>
+      from GenomicConsensus import reference
+    File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/reference.py", line
8, in <module>
+      from .windows import holes, kCoveredIntervals, enumerateIntervals
+    File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/windows.py", line 14,
in <module>
+      from ConsensusCore import CoveredIntervals
+  ImportError: No module named ConsensusCore
+  [1]

  There are two true SNVs (and one diploid SNV that we miss right now).

    $ grep insertion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep deletion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep substitution variants.gff
-
EGFR_Exon_23\t.\tsubstitution\t48\t48\t.\t.\t.\treference=T;variantSeq=C;frequency=97;coverage=100;confidence=40
(esc)
+  grep: variants.gff: No such file or directory
+  [2]
# Ran 1 tests, 0 skipped, 1 failed.
make: *** [Makefile:25: extra-tests] Error 1
autopkgtest [12:23:52]: test command2: -----------------------]
autopkgtest [12:23:52]: test command2:  - - - - - - - - - - results - -
- - - - - - - -
command2             FAIL non-zero exit status 2

Regards
Graham


[1] https://ci.debian.net/packages/p/pbgenomicconsensus/unstable/amd64/

Source: pbgenomicconsensus
Source-Version: 2.3.2-5

We believe that the bug you reported is fixed in the latest version of
pbgenomicconsensus, 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 [hidden email],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Liubov Chuprikova <[hidden email]> (supplier of updated pbgenomicconsensus 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 [hidden email])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Sun, 07 Apr 2019 13:58:37 +0200
Source: pbgenomicconsensus
Binary: pbgenomicconsensus python-pbgenomicconsensus
Architecture: source
Version: 2.3.2-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <[hidden email]>
Changed-By: Liubov Chuprikova <[hidden email]>
Description:
 pbgenomicconsensus - Pacific Biosciences variant and consensus caller
 python-pbgenomicconsensus - Pacific Biosciences variant and consensus caller (Python 2)
Closes: 925909
Changes:
 pbgenomicconsensus (2.3.2-5) unstable; urgency=medium
 .
   * Team upload.
   * Fix autopkgtest dependencies
     Closes: #925909
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 000ae613a5a54419564121511da922a75d1c04e6 20772 pbgenomicconsensus_2.3.2-5.debian.tar.xz
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 efd370ef90861470ea8c577c00e882a586722b7fe73eeba8fb6aaa08402e35ff 20772 pbgenomicconsensus_2.3.2-5.debian.tar.xz
Files:
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 5e418bfd3e208daf731fa54c3de52a81 20772 science optional pbgenomicconsensus_2.3.2-5.debian.tar.xz

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