Your message dated Sun, 08 May 2016 12:19:24 +0000
with message-id <[email protected]>
and subject line Bug#822701: fixed in samtools 1.3.1-2
has caused the Debian Bug report #822701,
regarding samtools 1.3 fails to build against htslib 1.3.1.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
822701: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822701
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: samtools
Version: 1.3-1
Severity: serious
Justification: fails to build from source
User: [email protected]
Usertags: ftbfs
X-Debbugs-Cc: [email protected]
Dear Maintainer,
samtools fails to build from source in unstable/amd64:
[..]
Generate CRAM file #2 .. ok
Generating test data file .................. done
Generate BAM file #3 .. ok
Generate CRAM file #3 .. ok
Generating test data file .................. done
Generate BAM file #4 .. ok
Generate CRAM file #4 .. ok
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
3: cat CRAM files .. ok
4: cat BAM files to stdout .. ok
5: cat recompressed BAM files to stdout .. ok
6: cat CRAM files to stdout .. ok
7: cat BAM files with new header .. ok
8: cat recompressed BAM files with new header .. ok
9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
Generate CRAM file .. ok
1: fastq (SAM input)
[M::bam2fq_mainloop] processed 36 reads
.. ok
2: fastq -n (SAM input)
[M::bam2fq_mainloop] processed 36 reads
.. ok
3: fastq (BAM input)
[M::bam2fq_mainloop] processed 36 reads
.. ok
4: fastq -n (BAM input)
[M::bam2fq_mainloop] processed 36 reads
.. ok
5: fastq (CRAM input)
[M::bam2fq_mainloop] processed 36 reads
.. ok
6: fastq -n (CRAM input)
[M::bam2fq_mainloop] processed 36 reads
.. ok
test_bam2fq:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fastq -1
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/1.fq
-2
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/2.fq
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fastq -s
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/s.fq
-1
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/1.fq
-2
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/2.fq
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fastq -s
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/s.fq
-1
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/1.fq
-2
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/2.fq
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/bam2fq.002.sam
.. ok
test_bam2fq:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fastq -s
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/s.fq
-1
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/1.fq
-2
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/2.fq
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/bam2fq.003.sam
.. ok
test_depad:
Generate BAM file .. ok
depad (SAM input) .. ok
depad -s (SAM input) .. ok
depad -u (SAM input) .. ok
depad -1 (SAM input) .. ok
depad (BAM input) .. ok
depad -s (BAM input) .. ok
depad -u (BAM input) .. ok
depad -1 (BAM input) .. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/1_map_cigar.sam
| tail -n+4
.. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/2_equal_cigar_full_seq.sam
| tail -n+4
.. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/3_map_cigar_equal_seq.sam
| tail -n+4
.. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/4_X_cigar_full_seq.sam
| tail -n+4
.. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/5_insert_cigar.sam
| tail -n+4
.. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
-i 0
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/5_insert_cigar.sam
| tail -n+4
.. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/7_supp.sam
| tail -n+4
.. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/8_secondary.sam
| tail -n+4
.. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -S RG -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/1_map_cigar.sam
| tail -n+4
.. ok
test_stats:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
stats -S RG -r
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/test.fa
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/stat/10_map_cigar.sam
| tail -n+4
.. ok
test_merge:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
merge -s 1 -
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_b.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_c.sam
.. ok
test_merge:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
merge -s 1 -
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a.bam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_b.bam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_c.bam
.. ok
test_merge:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
merge -s 1 -b /tmp/FjwTLcIMVX -
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a.bam
.. ok
test_merge:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
merge -s 1 -
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_b.bam
.. ok
test_merge:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
merge -r -s 1 -
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_b.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_c.sam
.. ok
test_merge:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
merge -cp -s 1 -
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_b.sam
.. ok
test_merge:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
merge -s 1 -
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a_regex.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_b_regex.sam
.. ok
test_sort:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
sort
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a.bam
/tmp/wocveQgKUk/sortout
.. ok
test_sort:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
sort -f
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a.bam
/tmp/wocveQgKUk/sortout.bam
.. ok
test_sort:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
sort -o
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a.bam
/tmp/wocveQgKUk/sorttmp
.. ok
test_fixmate:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fixmate -O sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/fixmate/1_coord_sort.sam
-
ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted
by queryname.
.. expected failure
test_fixmate:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fixmate -O sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/fixmate/2_isize_overflow.sam
-
.. ok
test_fixmate:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fixmate -O sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/fixmate/3_reverse_read_pp_lt.sam
-
.. ok
test_fixmate:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fixmate -O sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/fixmate/4_reverse_read_pp_equal.sam
-
.. ok
test_fixmate:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fixmate -cO sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/fixmate/5_ct.sam
-
.. ok
test_fixmate:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
fixmate -cO sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/fixmate/6_ct_replace.sam
-
.. ok
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
calmd -uAr
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/mpileup.1.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/mpileup.ref.fa
.. ok
test_idxstat:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
idxstats
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/test_input_1_a.bam
.. ok
test_quickcheck:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
quickcheck
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/quickcheck/1.quickcheck.badeof.bam
.. ok
test_quickcheck:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
quickcheck
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/quickcheck/2.quickcheck.badheader.bam
.. ok
test_quickcheck:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
quickcheck
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/quickcheck/3.quickcheck.ok.bam
.. ok
test_quickcheck:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
quickcheck
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/quickcheck/4.quickcheck.ok.bam
.. ok
test_quickcheck:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
quickcheck -v
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/quickcheck/1.quickcheck.badeof.bam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/quickcheck/2.quickcheck.badheader.bam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/quickcheck/3.quickcheck.ok.bam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/quickcheck/4.quickcheck.ok.bam
| sed 's,.*/quickcheck/,,'
.. ok
test_reheader:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
reheader
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/reheader/hdr.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/view.001.tmp.bam
|
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
view -h | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
reheader
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/reheader/hdr.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/view.001.tmp.v21.cram
|
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
view -h | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
reheader
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/reheader/hdr.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/view.001.tmp.v30.cram
|
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
view -h | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
reheader --in-place
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/reheader/hdr.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/view.001.tmp.v21.cram
&&
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
view -h
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/view.001.tmp.v21.cram
| perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
reheader --in-place
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/reheader/hdr.sam
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/view.001.tmp.v30.cram
&&
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
view -h
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/dat/view.001.tmp.v30.cram
| perl -pe 's/ VN:.*//'
.. ok
test_addrprg:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
addreplacerg -O sam -m overwrite_all
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
addreplacerg -O sam -m orphan_only
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
addreplacerg -O sam -R '1#7'
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC'
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
addreplacerg -O sam -m overwrite_all -R '1#8'
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/samtools
addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC'
/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3/test/addrprg/4_fixup_norg.sam
.. ok
Number of tests:
total .. 416
passed .. 398
failed .. 0
expected failure .. 18
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && ./regression.sh mpileup.reg
=== Testing mpileup.reg regressions ===
UNEXPECTED PASS: Task worked when we expected failure;
when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk
'{print $4}'
See PASS-47.out.1 vs expected/47.out
Expected passes: 123
Unexpected passes: 1
Expected failures: 0
Unexpected failures: 0
=> FAIL
Makefile:201: recipe for target 'test' failed
make[2]: *** [test] Error 1
make[2]: Leaving directory
'/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3'
dh_auto_test: make -j9 test VERBOSE=1 BGZIP=/usr/bin/bgzip returned exit code
2
debian/rules:25: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 2
make[1]: Leaving directory
'/home/lamby/temp/cdt.20160426185936.tgPyaYKRDx.samtools/samtools-1.3'
debian/rules:6: recipe for target 'build' failed
make: *** [build] Error 2
[..]
The full build log is attached.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` [email protected] / chris-lamb.co.uk
`-
samtools.1.3-1.unstable.amd64.log.txt.gz
Description: Binary data
--- End Message ---
--- Begin Message ---
Source: samtools
Source-Version: 1.3.1-2
We believe that the bug you reported is fixed in the latest version of
samtools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <[email protected]> (supplier of updated samtools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 08 May 2016 21:11:12 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: source
Version: 1.3.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Charles Plessy <[email protected]>
Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package
Closes: 822701
Changes:
samtools (1.3.1-2) unstable; urgency=medium
.
952da10 Build-depends on htslib 1.3.1. (Closes: #822701)
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samtools_1.3.1-2.debian.tar.xz
Files:
002bd04cff0c35c3938aed15ac48606c 2166 science optional samtools_1.3.1-2.dsc
71c6099d5e9bd6bd0620c56b7a8728af 11932 science optional
samtools_1.3.1-2.debian.tar.xz
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