[Debian-med-packaging] Samtools fails to build on several architectures [noreply at buildd.debian.org: failed i386 build of samtools 1.0-1]

Thu Sep 25 06:55:49 UTC 2014

Hi Charles,

On Thu, Sep 25, 2014 at 09:09:02AM +0900, Charles Plessy wrote:
> Brilliant, many thanks !

+1

> The issue was then quickly solved upstream.
> 
>     https://github.com/samtools/samtools/issues/300

I confirm that this problem is dealt with.  However, we remain at other
errors which are potentially of the same nature.  If you have a look at
the build log for i386[1] it ends up in

...
test_usage:
	samtools
test_view:
	Generating test data file .................. done
	1: SAM -> BAM -> SAM                                        
	SAM files differ at /tmp/PHZ6a904Ap/view.test001.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
	Failed command:
	/«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test001.bam -b /tmp/PHZ6a904Ap/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test001.bam.sam /tmp/PHZ6a904Ap/view.test001.bam

.. failed ...

	2: SAM -> uncompressed BAM                                  .. ok

	3: uncompressed BAM -> SAM and compare                      
	SAM files differ at /tmp/PHZ6a904Ap/view.test003.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
	Failed command:
	/«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test003.sam -h /tmp/PHZ6a904Ap/view.test002.bam

<more errors of this type here>

with a summary

Number of tests:
    total            .. 342
    passed           .. 237
    failed           .. 87
    expected failure .. 18
    unexpected pass  .. 0

When I try to build with pbuilder on an i386 machine I get at the point
copied above:

test_usage:                                                                                               
	samtools                                                                                          
test_view:                                                                                                
	Generating test data file .................. done                                                 
	1: SAM -> BAM -> SAM                                        .. ok                                 

	2: SAM -> uncompressed BAM                                  .. ok                                 

	3: uncompressed BAM -> SAM and compare                      .. ok                                 

	4: SAM -> fast compressed BAM                               .. ok                                 

	5: fast compressed BAM -> SAM and compare                   .. ok                                 

	6: SAM -> CRAM -> SAM (UR header tags)                      .. ok                                 

...
<no errors here>

with a summary:

Number of tests:                                                                                          
    total            .. 342                                                                               
    passed           .. 324                                                                               
    failed           .. 0                                                                                 
    expected failure .. 18                                                                                
    unexpected pass  .. 0                                                                                 

So it somehow gives the impression that on other arches (not only i386) the
terminal versus non-terminal environment remains at the unfortunate state to
cause errors in the test suite.

Any more ideas would be really welcome

      Andreas.

[1] https://buildd.debian.org/status/fetch.php?pkg=samtools&arch=i386&ver=1.1-1&stamp=1411604847

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