Re: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test

[Aurelien Jarno]

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

Re: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test

[Aurelien Jarno]

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


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Re: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test

[James Cowgill]

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



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Re: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test

[YunQiang Su]

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

Re: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test

[Emilio Pozuelo Monfort]

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.

> > 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