[Debian-med-packaging] gmap tests segfault on i386

[Alexander Mestiashvili]

Hi Andreas,

I've tried to build gmap again on my i386 virtualbox machine, but one of 
the tests segfaults.
There are no buildlogs for this package, so I can not check if it worked 
on i386 in the past.
Also I think because the package operates with huge datasets, it is not 
likely than anybody uses it on i386.
So how should we proceed ? upload to unstable anyway ?
I've submitted a bug report to upstream, but it seems we do not have 
time to wait for the answer for inclusion in jessy.

Thanks,
Alex

make  check-TESTS
make[1]: Entering directory '/tmp/gmap/tests'
GMAP version 2014-10-22 called with args: /tmp/gmap/src/gmap -A -g 
/tmp/gmap/tests/ss.chr17test /tmp/gmap/tests/ss.her2
Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1 
__builtin_ctz=0 __builtin_popcount=17
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Processed 1 queries in 0.44 seconds (2.27 queries/sec)
PASS: align.test
Opening file /tmp/gmap/tests/ss.chr17test
   Processed short contigs (<1000000 nt): .
============================================================
Contig mapping information has been written to file coords.chr17test.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
     make -f Makefile.chr17test gmapdb
============================================================
PASS: coords1.test
Sorting chromosomes in chrom order.  To turn off or sort other ways, use 
the -s flag.
Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1 
__builtin_ctz=0 __builtin_popcount=17
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Creating files in directory ./chr17test
Running /tmp/gmap/src/fa_coords    -o ./chr17test.coords -f 
./chr17test.sources
Opening file /tmp/gmap/tests/ss.chr17test
   Processed short contigs (<1000000 nt): .
============================================================
Contig mapping information has been written to file ./chr17test.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
     make gmapdb
============================================================
Running /tmp/gmap/src/gmap_process  -c ./chr17test.coords -f 
./chr17test.sources | /tmp/gmap/src/gmapindex  -d chr17test -D 
./chr17test -A
Reading coordinates from file ./chr17test.coords
Logging contig chr17test at chr17test:1..200000 in genome chr17test
Total genomic length = 200000 bp
Chromosome chr17test has universal coordinates 1..0
Writing IIT file header information...coordinates require 4 bytes 
each...done
Processing null division/chromosome...sorting...writing...done (1 intervals)
Writing IIT file footer information...done

Segmentation fault

/tmp/gmap/src/gmap_process  -c ./chr17test.coords -f ./chr17test.sources 
| /tmp/gmap/src/gmapindex  -d chr17test -D ./chr17test -A  failed with 
return code 35584 at /tmp/gmap/util/gmap_build line 269.
diff: ./chr17test/chr17test.genomecomp: No such file or directory
Difference found between chr17test.genomecomp and setup.genomecomp.ok
FAIL: setup1.test
Finished reading FASTA file -- total entries: 3
Maximum coordinate: 40000
Total label length: 3 + 0 separators
Total annotation length: 80 + 0 separators
Saw 0 distinct divisions/chromosomes
Saw 3 distinct tags/types
No divs/chromosomes provided, so storing as IIT version 1
Writing IIT file header information...coordinates require 4 bytes 
each...done
Processing null division/chromosome...sorting...writing...done (3 intervals)
Writing IIT file footer information...done