Source: samtools Version: 1.3-1 Severity: serious Justification: fails to build from source User: reproducible-builds@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-builds@lists.alioth.debian.org
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 `. `'` la...@debian.org / chris-lamb.co.uk `-
samtools.1.3-1.unstable.amd64.log.txt.gz
Description: Binary data
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