Source: rapmap Version: 0.5.0+dfsg-3 Severity: important Tags: upstream Justification: fails to build from source User: debian-m...@lists.debian.org 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 -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
