[Debian-med-packaging] Bug#826304: gmap: FTBFS in sid: 3 test fail

[Andreas Beckmann]

Source: gmap
Version: 2016-05-25-1
Severity: serious
Justification: fails to build from source

Hi,

gmap FTBFS in sid with testsuite failures:

   dh_auto_test -O--parallel
	make -j16 check VERBOSE=1
make[1]: Entering directory '/build/gmap-2016-05-25'
Making check in src
make[2]: Entering directory '/build/gmap-2016-05-25/src'
make[2]: Leaving directory '/build/gmap-2016-05-25/src'
Making check in util
make[2]: Entering directory '/build/gmap-2016-05-25/util'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/gmap-2016-05-25/util'
Making check in tests
make[2]: Entering directory '/build/gmap-2016-05-25/tests'
make  check-TESTS
make[3]: Entering directory '/build/gmap-2016-05-25/tests'
make[4]: Entering directory '/build/gmap-2016-05-25/tests'
FAIL: iit.test
FAIL: coords1.test
FAIL: setup1.test
PASS: align.test
===========================================
   gmap 2016-05-25: tests/test-suite.log
===========================================

# TOTAL: 4
# PASS:  1
# SKIP:  0
# XFAIL: 0
# FAIL:  3
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: coords1
=============

Cannot write to file coords.chr17test at /build/gmap-2016-05-25/util/fa_coords line 118.
Opening file /build/gmap-2016-05-25/tests/ss.chr17test
  Processed short contigs (<1000000 nt): .diff: coords.chr17test: No such file or directory
FAIL coords1.test (exit status: 2)

FAIL: setup1
============

Sorting chromosomes in chrom order.  To turn off or sort other ways, use the -s flag.
Could not create ./chr17test.sources at /build/gmap-2016-05-25/util/gmap_build line 155.
diff: ./chr17test/chr17test.genomecomp: No such file or directory
Difference found between chr17test.genomecomp and setup.genomecomp.ok
FAIL setup1.test (exit status: 1)

FAIL: iit
=========

mkdir: cannot create directory 'testSubDir': File exists
Finished reading FASTA file -- total entries: 3
Maximum coordinate: 40000
Total label length: 3 + 3 separators
Total annotation length: 80 + 3 separators
Saw 0 distinct divisions/chromosomes
Saw 3 distinct tags/types
No divs/chromosomes provided, so storing as IIT version 1
Error: can't open file iittest.iit
./iit.test: line 12: iit_get.out: No such file or directory
diff: iit_get.out: No such file or directory
./iit.test: line 15: iit_dump.out: No such file or directory
diff: iit_dump.out: No such file or directory
FAIL iit.test (exit status: 2)

============================================================================
Testsuite summary for gmap 2016-05-25
============================================================================
# TOTAL: 4
# PASS:  1
# SKIP:  0
# XFAIL: 0
# FAIL:  3
# XPASS: 0
# ERROR: 0
============================================================================
See tests/test-suite.log
Please report to Thomas Wu <twu at gene.com>
============================================================================
Makefile:575: recipe for target 'test-suite.log' failed
make[4]: *** [test-suite.log] Error 1
make[4]: Leaving directory '/build/gmap-2016-05-25/tests'
Makefile:681: recipe for target 'check-TESTS' failed
make[3]: *** [check-TESTS] Error 2
make[3]: Leaving directory '/build/gmap-2016-05-25/tests'
Makefile:747: recipe for target 'check-am' failed
make[2]: *** [check-am] Error 2
make[2]: Leaving directory '/build/gmap-2016-05-25/tests'
Makefile:430: recipe for target 'check-recursive' failed
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory '/build/gmap-2016-05-25'
dh_auto_test: make -j16 check VERBOSE=1 returned exit code 2
debian/rules:19: recipe for target 'build' failed
make: *** [build] Error 2


Andreas
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