Bug#887943: rapmap: FTBFS on mips64el: both tests fail

Source: rapmap
Version: 0.5.0+dfsg-3
Severity: important
Tags: upstream
Justification: fails to build from source
User: [email protected]
Usertags: mips64el

Builds of rapmap for mips64el have been failing, per the below excerpts from
https://buildd.debian.org/status/fetch.php?pkg=rapmap&arch=mips64el&ver=0.5.0%2Bdfsg-3&stamp=1516287344&raw=0.

Could you please take a look?  FWIW, "Bus error" (as reported by
quasi_map_test_ph) typically indicates unaligned memory access, which
some architectures enforce more strictly than others.

Thanks!

----------------------------------------------------------------------

Running tests...
/usr/bin/ctest --force-new-ctest-process -j4
Test project /<<BUILDDIR>>/rapmap-0.5.0+dfsg/obj-mips64el-linux-gnuabi64
    Start 1: quasi_map_test
    Start 2: quasi_map_test_ph
1/2 Test #1: quasi_map_test ...................***Failed    0.42 sec
RapMap Indexer

[Step 1 of 4] : counting k-mers
Elapsed time: 0.0297897s

Replaced 0 non-ATCG nucleotides
Clipped poly-A tails from 0 transcripts
Building rank-select dictionary and saving to disk done
Elapsed time: 5.0489e-05s
Writing sequence data to file . . . done
Elapsed time: 0.000206485s
[info] Building 32-bit suffix array (length of generalized text is 28577)
Building suffix array . . . success
saving to disk . . . done
Elapsed time: 0.000233346s
done
Elapsed time: 0.0113831s


processed 0 positionsCMake Error at /<<BUILDDIR>>/rapmap-0.5.0+dfsg/cmake/TestQuasiMap.cmake:8 (message):
  Error running



2/2 Test #2: quasi_map_test_ph ................***Failed    2.14 sec
RapMap Indexer

[Step 1 of 4] : counting k-mers
Elapsed time: 0.0370385s

Replaced 0 non-ATCG nucleotides
Clipped poly-A tails from 0 transcripts
Building rank-select dictionary and saving to disk done
Elapsed time: 0.000159219s
Writing sequence data to file . . . done
Elapsed time: 0.000300137s
[info] Building 32-bit suffix array (length of generalized text is 28577)
Building suffix array . . . success
saving to disk . . . done
Elapsed time: 0.000326992s
done
Elapsed time: 0.0119459s


processed 0 positions
[Building BooPHF]  0.989%   elapsed:   0 min 0  sec   remaining:   0 min 2  sec
[...]
[Building BooPHF]  100  %   elapsed:   0 min 0  sec   remaining:   0 min 0  sec
building perfect hash function
reordering keys and values to coincide with phf ... done
size of overflow table is 0

done.
saving the perfect hash and SA intervals to disk ... done.
[2018-01-18 14:55:31.625] [stderrLog] [info] 
command line options
====================
index: 
read(s) 1: reads_1.fastq
read(s) 2: reads_2.fastq
output: sample_quasi_map_ph.sam
num. threads: 2
max num. hits: 200
quasi-coverage: 0
no output: false
sensitive: false
strict check: true
fuzzy intersection: false
consistent hits: false
====================
[2018-01-18 14:55:31.627] [stderrLog] [info] Loading Suffix Array 
[2018-01-18 14:55:31.628] [stderrLog] [info] Loading Transcript Info 
[2018-01-18 14:55:31.628] [stderrLog] [info] Loading Rank-Select Bit Array
[2018-01-18 14:55:31.628] [stderrLog] [info] There were 15 set bits in the bit array
[2018-01-18 14:55:31.628] [stderrLog] [info] Computing transcript lengths
[2018-01-18 14:55:31.628] [stderrLog] [info] Waiting to finish loading hash
[2018-01-18 14:55:31.629] [stderrLog] [info] Done loading index




[2018-01-18 14:55:31.630] [stderrLog] [info] mapping reads . . . 





[2018-01-18 14:55:33.092] [stderrLog] [info] Done mapping reads.
[2018-01-18 14:55:33.092] [stderrLog] [info] In total saw 10000 reads.
[2018-01-18 14:55:33.092] [stderrLog] [info] Final # hits per read = 1.4253
[2018-01-18 14:55:33.092] [stderrLog] [info] flushing output queue.
Elapsed time: 1.46215s
CMake Error at /<<BUILDDIR>>/rapmap-0.5.0+dfsg/cmake/TestQuasiMapPerfectHash.cmake:17 (message):
  Error running Bus error




0% tests passed, 2 tests failed out of 2

Total Test time (real) =   2.17 sec

The following tests FAILED:
	  1 - quasi_map_test (Failed)
	  2 - quasi_map_test_ph (Failed)
Errors while running CTest
Makefile:143: recipe for target 'test' failed
make[1]: *** [test] Error 8
make[1]: Leaving directory '/<<BUILDDIR>>/rapmap-0.5.0+dfsg/obj-mips64el-linux-gnuabi64'
dh_auto_test: cd obj-mips64el-linux-gnuabi64 && make -j4 test ARGS\+=-j4 returned exit code 2
debian/rules:9: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2