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 -- http://fam-tille.de -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/[email protected]
