[Debian-med-packaging] Bug#814765: python-pysam: FTBFS: samtools index: "ex2_truncated.bam" is corrupted or unsorted

[Chris Lamb]

Source: python-pysam
Version: 0.8.4+ds-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org

Dear Maintainer,

python-pysam fails to build from source in unstable/amd64:

  [..]

  samtools index softclip.bam
  samtools index tag_bug.bam
  samtools index ex10.bam
  samtools index example_empty_header.bam
  samtools index test_unaligned.bam
  samtools index ex9_fail.bam
  samtools index issue100.bam
  samtools index ex5.bam
  samtools index ex6.bam
  samtools index rg_with_tab.bam
  samtools index ex9_nofail.bam
  samtools index example_btag.bam
  samtools index example_unmapped_reads_no_sq.bam
  samtools index ex4.bam
  samtools index example_user_header.bam
  samtools index ex8.bam
  samtools index ex3.bam
  samtools view -bC -T ex1.fa ex1.sam > ex1.cram
  samtools view -bC -T ex1.fa ex2.sam > ex2.cram
  samtools view -bC -T ex1.fa ex3.sam > ex3.cram
  samtools index ex1.cram
  samtools index ex2.cram
  samtools index ex3.cram
  cp ex1.bam example_bai.bam
  samtools index example_bai.bam
  mv example_bai.bam.bai example_bai.bai
  head -c 124000 ex2.bam > ex2_truncated.bam
  samtools index ex2_truncated.bam
  [W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
  samtools index: "ex2_truncated.bam" is corrupted or unsorted
  Makefile:48: recipe for target 'ex2_truncated.bam.bai' failed
  make[2]: *** [ex2_truncated.bam.bai] Error 1
  make[2]: Leaving directory '/home/lamby/temp/cdt.20160215090723.RznKM9ufGc/python-pysam-0.8.4+ds/tests/pysam_data'
  debian/rules:26: recipe for target 'override_dh_auto_test' failed
  make[1]: *** [override_dh_auto_test] Error 2
  make[1]: Leaving directory '/home/lamby/temp/cdt.20160215090723.RznKM9ufGc/python-pysam-0.8.4+ds'
  debian/rules:20: recipe for target 'build' failed
  make: *** [build] Error 2

  [..]

The full build log is attached.


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-
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