[Debian-med-packaging] Bug#774109: htslib: FTBFS on hppa

[John David Anglin]

Package: htslib
Version: 1.1-1
Severity: normal

Tests fail:

=== Testing aux#aux.sam, ref aux.fa ===
  ./test_view -S -b aux#aux.sam > aux#aux.tmp.bam
  ./test_view aux#aux.tmp.bam > aux#aux.tmp.bam.sam_
  ./compare_sam.pl aux#aux.sam aux#aux.tmp.bam.sam_
  ./test_view -t aux.fa -S -C aux#aux.sam > aux#aux.tmp.cram
Bus error
FAIL 

Full log:
http://buildd.debian-ports.org/status/fetch.php?pkg=htslib&arch=hppa&ver=1.1-1&stamp=1411592339

hppa is big endian.  The cram_encode.c portion of the mips 01-fix-endianness.patch patch fixes this bus error.  However, the sam.c portion no longer applies.

With the 01-fix-endianness.patch patch, things fail here:

Failures  0
cd test && ./test.pl
test_vcf_api:
	/«PKGBUILDDIR»/test/test-vcf-api /tmp/hzVl69JfEW/test-vcf-api.bcf

	The outputs differ:
		/«PKGBUILDDIR»/test/test-vcf-api.out
		/«PKGBUILDDIR»/test/test-vcf-api.out.new
.. failed ...



-- System Information:
Debian Release: 8.0
  APT prefers unreleased
  APT policy: (500, 'unreleased'), (500, 'unstable')
Architecture: hppa (parisc64)

Kernel: Linux 3.17.7+ (SMP w/4 CPU cores)
Locale: LANG=C, LC_CTYPE=C (charmap=UTF-8) (ignored: LC_ALL set to en_CA.utf8)
Shell: /bin/sh linked to /bin/dash
Init: sysvinit (via /sbin/init)