Bug#859111: [Debian-med-packaging] Bug#859111: Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
tags 859111 pending thanks > bowtie2 2.3.1 introduced different default values for one of the > parameters [1], it might be likely that it's connected to that. I > have contacted upstream Upstream have added support for Bowtie2 2.3.1 [1] and I can confirm that the tests -- and hence the build -- are fixed using this latest version. Updated Debian package currently in experimental, will upload to unstable once the freeze is over. Cheers Sascha [1] https://github.com/sanger-pathogens/ariba/issues/170 signature.asc Description: OpenPGP digital signature
Processed: Re: [Debian-med-packaging] Bug#859111: Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
Processing commands for cont...@bugs.debian.org: > tags 859111 pending Bug #859111 [src:ariba] ariba FTBFS with bowtie2 2.3.1-1 Added tag(s) pending. > thanks Stopping processing here. Please contact me if you need assistance. -- 859111: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=859111 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Bug#859111: [Debian-med-packaging] Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
forwarded 859111 https://github.com/sanger-pathogens/ariba/issues/170 tags 859111 upstream thanks Hi all, > On Thu, Mar 30, 2017 at 06:20:16PM +0300, Adrian Bunk wrote: >> Control: retitle -1 ariba FTBFS with bowtie2 2.3.1-1 > [...] >> This is actually not related to the ariba version but to the bowtie2 version, >> ariba 2.6.1+ds-1 in stretch builds with the stretch bowtie2 2.3.0-2 but >> FTBFS with the sid bowtie2 2.3.1-1 > > Do we already know whether the newer upstream version fixes this? No, it doesn't. I just tested it. Given that the test failure seems to be caused by differences between result and reference, and bowtie2 2.3.1 introduced different default values for one of the parameters [1], it might be likely that it's connected to that. I have contacted upstream [2] -- they are usually quite responsive. Cheers Sascha [1] http://bowtie-bio.sourceforge.net/bowtie2/index.shtml [2] https://github.com/sanger-pathogens/ariba/issues/170
Processed: Re: [Debian-med-packaging] Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
Processing commands for cont...@bugs.debian.org: > forwarded 859111 https://github.com/sanger-pathogens/ariba/issues/170 Bug #859111 [src:ariba] ariba FTBFS with bowtie2 2.3.1-1 Set Bug forwarded-to-address to 'https://github.com/sanger-pathogens/ariba/issues/170'. > tags 859111 upstream Bug #859111 [src:ariba] ariba FTBFS with bowtie2 2.3.1-1 Added tag(s) upstream. > thanks Stopping processing here. Please contact me if you need assistance. -- 859111: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=859111 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Bug#859111: [Debian-med-packaging] Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
Hi all, >> Control: retitle -1 ariba FTBFS with bowtie2 2.3.1-1 > [...] >> This is actually not related to the ariba version but to the bowtie2 version, >> ariba 2.6.1+ds-1 in stretch builds with the stretch bowtie2 2.3.0-2 but >> FTBFS with the sid bowtie2 2.3.1-1 > > Do we already know whether the newer upstream version fixes this? > > Sascha: could you try to import it and pehaps upload it to unstable? > Given there is already a difference between testing and unstable (2.6.1 > vs 2.7.1) it shouldn't make much difference at this point even in the > freeze… Sure, I can do this later today when I find some time. I'm a bit busy atm with unrelated work but will get back to it. Cheers Sascha signature.asc Description: OpenPGP digital signature
Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
On Thu, Mar 30, 2017 at 06:20:16PM +0300, Adrian Bunk wrote: > Control: retitle -1 ariba FTBFS with bowtie2 2.3.1-1 [...] > This is actually not related to the ariba version but to the bowtie2 version, > ariba 2.6.1+ds-1 in stretch builds with the stretch bowtie2 2.3.0-2 but > FTBFS with the sid bowtie2 2.3.1-1 Do we already know whether the newer upstream version fixes this? Sascha: could you try to import it and pehaps upload it to unstable? Given there is already a difference between testing and unstable (2.6.1 vs 2.7.1) it shouldn't make much difference at this point even in the freeze… -- regards, Mattia Rizzolo GPG Key: 66AE 2B4A FCCF 3F52 DA18 4D18 4B04 3FCD B944 4540 .''`. more about me: https://mapreri.org : :' : Launchpad user: https://launchpad.net/~mapreri `. `'` Debian QA page: https://qa.debian.org/developer.php?login=mattia `- signature.asc Description: PGP signature
Processed: Re: Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
Processing control commands: > found -1 2.6.1+ds-1 Bug #859111 [src:ariba] ariba: FTBFS: FAIL: Test run_bowtie2 unsorted Marked as found in versions ariba/2.6.1+ds-1. > retitle -1 ariba FTBFS with bowtie2 2.3.1-1 Bug #859111 [src:ariba] ariba: FTBFS: FAIL: Test run_bowtie2 unsorted Changed Bug title to 'ariba FTBFS with bowtie2 2.3.1-1' from 'ariba: FTBFS: FAIL: Test run_bowtie2 unsorted'. > tags -1 sid Bug #859111 [src:ariba] ariba FTBFS with bowtie2 2.3.1-1 Added tag(s) sid. -- 859111: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=859111 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
Control: found -1 2.6.1+ds-1 Control: retitle -1 ariba FTBFS with bowtie2 2.3.1-1 Control: tags -1 sid On Thu, Mar 30, 2017 at 01:46:26PM +0100, Chris Lamb wrote: > Source: ariba > Version: 2.7.1+ds-1 >... > == > FAIL: Test run_bowtie2 unsorted > -- >... This is actually not related to the ariba version but to the bowtie2 version, ariba 2.6.1+ds-1 in stretch builds with the stretch bowtie2 2.3.0-2 but FTBFS with the sid bowtie2 2.3.1-1 The Debian Med team should know better which of the packages need fixing. I am tagging this bug "sid" since bowtie2 2.3.1-1 is anyway not supposed to ever enter stretch, so there seems to be nothing that needs fixing for stretch. cu Adrian -- "Is there not promise of rain?" Ling Tan asked suddenly out of the darkness. There had been need of rain for many days. "Only a promise," Lao Er said. Pearl S. Buck - Dragon Seed
Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
Source: ariba
Version: 2.7.1+ds-1
Severity: serious
Justification: fails to build from source
User: reproducible-bui...@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-b...@lists.alioth.debian.org
Dear Maintainer,
ariba fails to build from source in unstable/amd64:
[…]
==
FAIL: Test run_bowtie2 unsorted
--
Traceback (most recent call last):
File "«BUILDDIR»/ariba/tests/mapping_test.py", line 61, in test_run_bowtie2
self.assertListEqual(expected, got)
AssertionError: Lists differ: [('1', 99, 'ref', 0, [(4, 5), (0, 20)],
'AGCCCTC[857 chars]AT')] != [('1', 153, 'ref', 30, [(0, 25)],
'AGGATACAGATCT[794 chars]AT')]
First differing element 0:
('1', 99, 'ref', 0, [(4, 5), (0, 20)], 'AGCCCTCCACAGGATGGTGGTATAC')
('1', 153, 'ref', 30, [(0, 25)], 'AGGATACAGATCTTGTGGGAAAGGT')
- [('1', 99, 'ref', 0, [(4, 5), (0, 20)], 'AGCCCTCCACAGGATGGTGGTATAC'),
- ('1', 147, 'ref', 30, [(0, 25)], 'AGGATACAGATCTTGTGGGAAAGGT'),
? ^ ^^
+ [('1', 153, 'ref', 30, [(0, 25)], 'AGGATACAGATCTTGTGGGAAAGGT'),
? ^ ^^
+ ('1', 69, None, 30, [], 'AGCCCTCCACAGGATGGTGGTATAC'),
- ('2', 99, 'ref', 124, [(0, 25)], 'TAATGTTCTTAGGGCTTACCATAGA'),
?^^
+ ('2', 73, 'ref', 124, [(0, 25)], 'TAATGTTCTTAGGGCTTACCATAGA'),
?^^
- ('2', 147, 'ref', 170, [(0, 20), (4, 5)], 'TCCACCTTAGCTAAGCGCAGACTCG'),
+ ('2', 133, None, 124, [], 'CGAGTCTGCGCTTAGCTAAGGTGGA'),
('3', 73, 'ref', 86, [(0, 25)], 'TCGGGTCTGTACAAGGACGGATGGT'),
('3', 133, None, 86, [], 'CGTACTGACTGACTGACGTACTGCA'),
('4', 99, 'ref', 55, [(0, 25)], 'CCGCCGGGAAGTCCTTCTGTCGTGC'),
('4', 147, 'ref', 136, [(0, 25)], 'GGCTTACCATAGAGGTACACT'),
- ('5', 99, 'ref', 0, [(4, 2), (0, 23)], 'CCTCCACAGGATGGTGGTATACCTG'),
?^^ ^^ -- ^ ---
+ ('5', 77, None, -1, [], 'CCTCCACAGGATGGTGGTATACCTG'),
?^^ ^^^ ^^
- ('5', 147, 'ref', 166, [(0, 24), (4, 1)], 'TTCATCCACCTTAGCTAAGCGCAGA'),
+ ('5', 141, None, -1, [], 'TCTGCGCTTAGCTAAGGTGGATGAA'),
('6', 77, None, -1, [], 'CAGTTGCATGACGTCATGCAGTCAT'),
('6', 141, None, -1, [], 'AATGAGTATGATGAGTAATGGTATG'),
('7', 99, 'ref', 56, [(4, 1), (0, 23), (4, 1)],
'ACGCCGGGAAGTCCTTCTGTCGTGT'),
('7', 147, 'ref', 136, [(0, 24), (4, 1)], 'GGCTTACCATAGAGGTACACTAAAT')]
==
FAIL: Test run_bowtie2 sorted
--
Traceback (most recent call last):
File "«BUILDDIR»/ariba/tests/mapping_test.py", line 102, in
test_run_bowtie2_and_sort
self.assertListEqual(expected, got)
AssertionError: Lists differ: [('1', 99, 'ref', 0, [(4, 5), (0, 20)],
'AGCCCTC[857 chars]TG')] != [('1', 69, None, 30, [],
'AGCCCTCCACAGGATGGTGGTA[794 chars]TG')]
First differing element 0:
('1', 99, 'ref', 0, [(4, 5), (0, 20)], 'AGCCCTCCACAGGATGGTGGTATAC')
('1', 69, None, 30, [], 'AGCCCTCCACAGGATGGTGGTATAC')
Diff is 1432 characters long. Set self.maxDiff to None to see it.
--
Ran 317 tests in 59.987s
FAILED (failures=2)
debian/rules:23: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '«BUILDDIR»'
debian/rules:10: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
[…]
The full build log is attached.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` la...@debian.org / chris-lamb.co.uk
`-
ariba.2.7.1+ds-1.unstable.amd64.log.txt.gz
Description: Binary data
