Bug#834856: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test
control: severity -1 important control: retitle -1 python-pysam: FTBFS on 32-bit architectures: segmentation fault in testsuite On 2016-10-23 12:25, Emilio Pozuelo Monfort wrote: > On 23/10/16 00:48, Aurelien Jarno wrote: > > On 2016-10-21 15:15, James Cowgill wrote: > >> On 21/10/16 14:55, YunQiang Su wrote: > >>> On Fri, Oct 14, 2016 at 3:47 PM, Emilio Pozuelo Monfort > >>> wrote: > Control: severity -1 serious > > On Fri, 19 Aug 2016 22:29:48 -0700 Afif Elghraoui > wrote: > > Control: severity -1 important > > Control: tag -1 + help > > > > Hello and thank you for the report. > > > > على الجمعـة 19 آب 2016 ‫14:48، كتب Jonathan Jackson: > >> Package: python-pysam > >> Version: 0.9.1.4+ds-1 > >> Severity: grave > >> Justification: renders package unusable > >> > > > > While the package may be unusable on mips64el, it works well for the > > vast majority of users as I understand it, so this situation deserves a > > severity of 'important' rather than 'grave'. > > mips64el is a release architecture, thus this bug is serious. > >>> > >>> mips64el seems building successfully now, while mipsel fails. > >>> I guess it is due to Loongson machine. > >> > >> If mips64el has built (possibly one of the build machines is 'nicer' to > >> it), is this bug RC anymore? > >> > >>> Let me have a give-back on mipsel. > >> > >> While it could help, the same segfault happens on armel, mipsel and x32 > >> according to the build logs. I don't think it's hardware specific. > >> > >> https://buildd.debian.org/status/package.php?p=python-pysam > > > > I agree with this analysis. I confirm it doesn't build either on > > eller.d.o and from what I have been able to start debugging with GDB, it > > rather looks like some bug in the 32-bit support. There is something > > wrong in htslib or the cython code which doesn't convert C struct into > > Python struct correctly. > > > > I therefore also suggest to downgrade the severity of this bug, maybe > > also retitling it to say it fail to all 32-bit architectures. > > Sounds good. > Ok, doing so with this mail. Aurelien -- Aurelien Jarno GPG: 4096R/1DDD8C9B aurel...@aurel32.net http://www.aurel32.net
Bug#834856: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test
On 23/10/16 00:48, Aurelien Jarno wrote: > On 2016-10-21 15:15, James Cowgill wrote: >> On 21/10/16 14:55, YunQiang Su wrote: >>> On Fri, Oct 14, 2016 at 3:47 PM, Emilio Pozuelo Monfort >>> wrote: Control: severity -1 serious On Fri, 19 Aug 2016 22:29:48 -0700 Afif Elghraoui wrote: > Control: severity -1 important > Control: tag -1 + help > > Hello and thank you for the report. > > على الجمعـة 19 آب 2016 ‫14:48، كتب Jonathan Jackson: >> Package: python-pysam >> Version: 0.9.1.4+ds-1 >> Severity: grave >> Justification: renders package unusable >> > > While the package may be unusable on mips64el, it works well for the > vast majority of users as I understand it, so this situation deserves a > severity of 'important' rather than 'grave'. mips64el is a release architecture, thus this bug is serious. >>> >>> mips64el seems building successfully now, while mipsel fails. >>> I guess it is due to Loongson machine. >> >> If mips64el has built (possibly one of the build machines is 'nicer' to >> it), is this bug RC anymore? >> >>> Let me have a give-back on mipsel. >> >> While it could help, the same segfault happens on armel, mipsel and x32 >> according to the build logs. I don't think it's hardware specific. >> >> https://buildd.debian.org/status/package.php?p=python-pysam > > I agree with this analysis. I confirm it doesn't build either on > eller.d.o and from what I have been able to start debugging with GDB, it > rather looks like some bug in the 32-bit support. There is something > wrong in htslib or the cython code which doesn't convert C struct into > Python struct correctly. > > I therefore also suggest to downgrade the severity of this bug, maybe > also retitling it to say it fail to all 32-bit architectures. Sounds good. Emilio
Bug#834856: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test
On 2016-10-21 15:15, James Cowgill wrote: > On 21/10/16 14:55, YunQiang Su wrote: > > On Fri, Oct 14, 2016 at 3:47 PM, Emilio Pozuelo Monfort > > wrote: > >> Control: severity -1 serious > >> > >> On Fri, 19 Aug 2016 22:29:48 -0700 Afif Elghraoui wrote: > >>> Control: severity -1 important > >>> Control: tag -1 + help > >>> > >>> Hello and thank you for the report. > >>> > >>> على الجمعـة 19 آب 2016 ‫14:48، كتب Jonathan Jackson: > Package: python-pysam > Version: 0.9.1.4+ds-1 > Severity: grave > Justification: renders package unusable > > >>> > >>> While the package may be unusable on mips64el, it works well for the > >>> vast majority of users as I understand it, so this situation deserves a > >>> severity of 'important' rather than 'grave'. > >> > >> mips64el is a release architecture, thus this bug is serious. > > > > mips64el seems building successfully now, while mipsel fails. > > I guess it is due to Loongson machine. > > If mips64el has built (possibly one of the build machines is 'nicer' to > it), is this bug RC anymore? > > > Let me have a give-back on mipsel. > > While it could help, the same segfault happens on armel, mipsel and x32 > according to the build logs. I don't think it's hardware specific. > > https://buildd.debian.org/status/package.php?p=python-pysam I agree with this analysis. I confirm it doesn't build either on eller.d.o and from what I have been able to start debugging with GDB, it rather looks like some bug in the 32-bit support. There is something wrong in htslib or the cython code which doesn't convert C struct into Python struct correctly. I therefore also suggest to downgrade the severity of this bug, maybe also retitling it to say it fail to all 32-bit architectures. -- Aurelien Jarno GPG: 4096R/1DDD8C9B aurel...@aurel32.net http://www.aurel32.net signature.asc Description: PGP signature
Bug#834856: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test
On 21/10/16 14:55, YunQiang Su wrote: > On Fri, Oct 14, 2016 at 3:47 PM, Emilio Pozuelo Monfort > wrote: >> Control: severity -1 serious >> >> On Fri, 19 Aug 2016 22:29:48 -0700 Afif Elghraoui wrote: >>> Control: severity -1 important >>> Control: tag -1 + help >>> >>> Hello and thank you for the report. >>> >>> على الجمعـة 19 آب 2016 ‫14:48، كتب Jonathan Jackson: Package: python-pysam Version: 0.9.1.4+ds-1 Severity: grave Justification: renders package unusable >>> >>> While the package may be unusable on mips64el, it works well for the >>> vast majority of users as I understand it, so this situation deserves a >>> severity of 'important' rather than 'grave'. >> >> mips64el is a release architecture, thus this bug is serious. > > mips64el seems building successfully now, while mipsel fails. > I guess it is due to Loongson machine. If mips64el has built (possibly one of the build machines is 'nicer' to it), is this bug RC anymore? > Let me have a give-back on mipsel. While it could help, the same segfault happens on armel, mipsel and x32 according to the build logs. I don't think it's hardware specific. https://buildd.debian.org/status/package.php?p=python-pysam Thanks, James signature.asc Description: OpenPGP digital signature
Bug#834856: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test
On Fri, Oct 14, 2016 at 3:47 PM, Emilio Pozuelo Monfort wrote: > Control: severity -1 serious > > On Fri, 19 Aug 2016 22:29:48 -0700 Afif Elghraoui wrote: >> Control: severity -1 important >> Control: tag -1 + help >> >> Hello and thank you for the report. >> >> على الجمعـة 19 آب 2016 ‫14:48، كتب Jonathan Jackson: >> > Package: python-pysam >> > Version: 0.9.1.4+ds-1 >> > Severity: grave >> > Justification: renders package unusable >> > >> >> While the package may be unusable on mips64el, it works well for the >> vast majority of users as I understand it, so this situation deserves a >> severity of 'important' rather than 'grave'. > > mips64el is a release architecture, thus this bug is serious. mips64el seems building successfully now, while mipsel fails. I guess it is due to Loongson machine. Let me have a give-back on mipsel. > >> > Python-pysam packages failed to build on March 24th on a mips64el >> > architecture. Here is the tail of the failed-build log: >> > >> [...] >> >> I'd be happy to apply any patch that resolves this problem, but porting >> work is beyond what I can commit to do for this package. > > Cc'ing debian-mips, maybe they can provide some help. > > Cheers, > Emilio > -- YunQiang Su
Bug#834856: Should we exclude mips64el? (Was: Bug#834856: python-pysam fails to build on mips64el arch.: failed test)
Hi, as Afif said before in the Debian Med team we do not have any capacity to track down mips specific bugs. The only clue we had would be to remove the package from mips64el which would be a shame but for the time beeing would reflect the practical usage of the package which is basically amd64. Kind regards Andreas. -- http://fam-tille.de
Bug#834856: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test
Control: severity -1 serious On Fri, 19 Aug 2016 22:29:48 -0700 Afif Elghraoui wrote: > Control: severity -1 important > Control: tag -1 + help > > Hello and thank you for the report. > > عÙ٠اÙج٠عÙØ© 19 آب 2016 â«14:48Ø Ùتب Jonathan Jackson: > > Package: python-pysam > > Version: 0.9.1.4+ds-1 > > Severity: grave > > Justification: renders package unusable > > > > While the package may be unusable on mips64el, it works well for the > vast majority of users as I understand it, so this situation deserves a > severity of 'important' rather than 'grave'. mips64el is a release architecture, thus this bug is serious. > > Python-pysam packages failed to build on March 24th on a mips64el > > architecture. Here is the tail of the failed-build log: > > > [...] > > I'd be happy to apply any patch that resolves this problem, but porting > work is beyond what I can commit to do for this package. Cc'ing debian-mips, maybe they can provide some help. Cheers, Emilio
Bug#834856: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test
Control: severity -1 important Control: tag -1 + help Hello and thank you for the report. على الجمعـة 19 آب 2016 14:48، كتب Jonathan Jackson: > Package: python-pysam > Version: 0.9.1.4+ds-1 > Severity: grave > Justification: renders package unusable > While the package may be unusable on mips64el, it works well for the vast majority of users as I understand it, so this situation deserves a severity of 'important' rather than 'grave'. > > Python-pysam packages failed to build on March 24th on a mips64el > architecture. Here is the tail of the failed-build log: > [...] I'd be happy to apply any patch that resolves this problem, but porting work is beyond what I can commit to do for this package. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Bug#834856: python-pysam fails to build on mips64el arch.: failed test
Package: python-pysam
Version: 0.9.1.4+ds-1
Severity: grave
Justification: renders package unusable
Dear Maintainer,
Python-pysam packages failed to build on March 24th on a mips64el
architecture. Here is the tail of the failed-build log:
>testAlt (VariantFile_test.TestParsing) ... ok
>testChrom (VariantFile_test.TestParsing) ... ok
>testFilter (VariantFile_test.TestParsing) ... ok
>testFormat (VariantFile_test.TestParsing) ... ok
>testId (VariantFile_test.TestParsing) ... ok
>testInfo (VariantFile_test.TestParsing) ... Illegal instruction
>E: pybuild pybuild:274: test: plugin distutils failed with: exit code=132: cd
>/«BUILDDIR»/python-pysam-0.9.1.4+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m
>nose
>dh_auto_test: pybuild --test -i python{version} -p 2.7 returned exit code 13
>debian/rules:36: recipe for target 'override_dh_auto_test' failed
>make[1]: *** [override_dh_auto_test] Error 25
>make[1]: Leaving directory '/«BUILDDIR»/python-pysam-0.9.1.4+ds'
>debian/rules:30: recipe for target 'build-arch' failed
>make: *** [build-arch] Error 2
>dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
Precise cause of failure during "testInfo" is unknown atm.
Here is a link to the full failed-build log:
https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=mips64el&ver=0.9.1.4%2Bds-1&stamp=1469339179
Thank you,
Jonathan Jackson
-- System Information:
Package: python-pysam 0.9.1.4+ds-1
Version: 0.9.1.4+ds-1
Source Version: 0.9.1.4+ds-1
Distribution: sid
Machine Architecture: mipsel
Host Architecture: mips64el
Build Architecture: mips64el
