ffranr
commented
6 years ago What version of autoconf is used? It might need updating.
Closed iqbal-lab closed 6 years ago
ffranr
commented
6 years ago What version of autoconf is used? It might need updating.
iqbal-lab
commented
6 years ago autoconf --version autoconf (GNU Autoconf) 2.63
ffranr
commented
6 years ago These are the key lines:
[ 33%] Performing configure step for 'htslib'
configure.ac:26: error: possibly undefined macro: m4_esyscmd_s
If this token and others are legitimate, please use m4_pattern_allow.
See the Autoconf documentation.
make[2]: *** [libgramtools/htslib-prefix/src/htslib-stamp/htslib-configure] Error 1
make[1]: *** [libgramtools/CMakeFiles/htslib.dir/all] Error 2Install pkg-config source: https://github.com/tmux/tmux/issues/257
Install libtool (apt-get install libtool) source: https://github.com/sanger-pathogens/gubbins/issues/130
iqbal-lab
commented
6 years ago Thanks, talking to sysadmins in Oxford
ffranr
commented
6 years ago This is how gramtools attempts to install htslib from source:
execute_process(COMMAND mkdir -p ${CMAKE_CURRENT_BINARY_DIR}/src/htslib-1.6)
ExternalProject_Add(htslib
DOWNLOAD_COMMAND wget https://github.com/samtools/htslib/releases/download/1.6/htslib-1.6.tar.bz2 --timestamping
DOWNLOAD_DIR "${CMAKE_CURRENT_BINARY_DIR}/download"
CONFIGURE_COMMAND bash -c "cd ${CMAKE_CURRENT_BINARY_DIR}/src/htslib-1.6 && autoheader && autoconf && env CPPFLAGS=-I${CMAKE_CURRENT_BINARY_DIR}/include LDFLAGS=-L${CMAKE_CURRENT_BINARY_DIR}/lib ./configure --prefix=${CMAKE_CURRENT_BINARY_DIR}"
BUILD_COMMAND bash -c "cd ${CMAKE_CURRENT_BINARY_DIR}/src/htslib-1.6 && make && make install"
INSTALL_COMMAND ""
TEST_COMMAND "")
ExternalProject_Add_Step(htslib extract_tar
COMMAND tar -xjf ${CMAKE_CURRENT_BINARY_DIR}/download/htslib-1.6.tar.bz2 -C ${CMAKE_CURRENT_BINARY_DIR}/src
DEPENDEES download
DEPENDERS configure)htslib should be able to be installed manually using similar commands.
iqbal-lab
commented
6 years ago Right, so this helped
module load autoconf/2.69
and got me much further.
Now dealing with this
checking for lzma_easy_buffer_encode in -llzma... no configure: error: liblzma development files not found
The CRAM format may use LZMA2 compression, which is implemented in HTSlib
by using compression routines from liblzma <http://tukaani.org/xz/>.
Building HTSlib requires liblzma development files to be installed on the
build machine; you may need to ensure a package such as liblzma-dev (on Debian
or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
xz (via Homebrew on macOS) is installed; or build XZ Utils from source.OK, a bunch of progress. Had to install a few things, and now we break here
Tests in the test-directory
A cheat sheet in the extras/cheatsheet-directory.
Have fun!
[ 49%] No install step for 'sdsl'
[ 50%] No test step for 'sdsl'
[ 51%] Completed 'sdsl'
[ 51%] Built target sdsl
Scanning dependencies of target gramtools
[ 53%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/search.cpp.o
/tmp/pip-ealvtjfy-build/libgramtools/src/search.cpp: In function ‘std::__cxx11::string serialize_search_state(const SearchState&)’:
/tmp/pip-ealvtjfy-build/libgramtools/src/search.cpp:582:41: warning: switch condition has type bool [-Wswitch-bool]
switch (search_state.cache_populated) {
^
[ 54%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/utils.cpp.o
[ 55%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/quasimap/quasimap.cpp.o
[ 57%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/quasimap/utils.cpp.o
[ 58%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/quasimap/coverage/common.cpp.o
[ 59%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/quasimap/coverage/allele_sum.cpp.o
[ 61%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/quasimap/coverage/allele_base.cpp.o
[ 62%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/quasimap/coverage/grouped_allele_counts.cpp.o
[ 63%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/kmer_index/kmers.cpp.o
[ 64%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/kmer_index/kmer_index.cpp.o
[ 66%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/prg/prg.cpp.o
[ 67%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/prg/masks.cpp.o
[ 68%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/prg/dna_ranks.cpp.o
[ 70%] Building CXX object libgramtools/CMakeFiles/gramtools.dir/src/prg/fm_index.cpp.o
[ 71%] Linking CXX static library ../lib/libgramtools.a
[ 71%] Built target gramtools
Scanning dependencies of target gram
[ 72%] Building CXX object libgramtools/CMakeFiles/gram.dir/src/main.cpp.o
[ 74%] Building CXX object libgramtools/CMakeFiles/gram.dir/src/timer_report.cpp.o
[ 75%] Linking CXX executable ../bin/gram
/tmp/pip-ealvtjfy-build/cmake-build-debug/libgramtools/lib/libboost_chrono.a(chrono.o): In function `boost::chrono::system_clock::now()':
chrono.cpp:(.text+0xa): undefined reference to `clock_gettime'
/tmp/pip-ealvtjfy-build/cmake-build-debug/libgramtools/lib/libboost_chrono.a(chrono.o): In function `boost::chrono::steady_clock::now()':
chrono.cpp:(.text+0x6d): undefined reference to `clock_gettime'
/tmp/pip-ealvtjfy-build/cmake-build-debug/libgramtools/lib/libboost_chrono.a(chrono.o): In function `boost::chrono::system_clock::now(boost::system::error_code&)':
chrono.cpp:(.text+0x9f): undefined reference to `clock_gettime'
/tmp/pip-ealvtjfy-build/cmake-build-debug/libgramtools/lib/libboost_chrono.a(chrono.o): In function `boost::chrono::steady_clock::now(boost::system::error_code&)':
chrono.cpp:(.text+0x152): undefined reference to `clock_gettime'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/gram] Error 1
make[1]: *** [libgramtools/CMakeFiles/gram.dir/all] Error 2
make: *** [all] Error 2
error: [Errno 2] No such file or directory: '/localhome/tmp/pip-ealvtjfy-build/cmake-build-debug/libgramtools/tests/test_main'Jon (sysadmin) says
"You need an additional ' -lrt' appended to the linker arguments on el6 - that method subsequently moved into glibc (as of glibc 2.17), so you don't need it on a newer OS."
I asked what el6 was, and he said
"RedHat Enterprise Linux 6 - on which CentOS 6 is based. Abbreviated to 'el6'"
Robyn - is there a way to detect this (which glibc we have I mean)? Not sure where to put the -lrt
ffranr
commented
6 years ago The version of glibc can be found by executing ldd --version. I have glibc 2.24 on my ubuntu machine.
Supporting older versions of glibc would require adding -lrt to the cmake file. I'm not sure if that solution is suitable for modern systems also. I will look into it. The cmake file is not easily accessible when installing gramtools with pip.
Here's an example of where to add -lrt:
https://stackoverflow.com/questions/13653361/another-undefined-reference-error-when-linking-boost-libraries
glibc 2.17 was released in 2012.
iqbal-lab
commented
6 years ago I think we have to face the facts that we can't make our users all have up to date OS's. My server in Oxford is not unusual.
ldd --version ldd (GNU libc) 2.12
ffranr
commented
6 years ago I've pushed changes which should fix this issue. I've added -lrt as a compiler flag.
iqbal-lab
commented
6 years ago God bless you, sorry for this
iqbal-lab
commented
6 years ago OK that worked, now I have this
[ 73%] Building CXX object libgramtools/CMakeFiles/gram.dir/src/timer_report.cpp.o
[ 74%] Linking CXX executable ../bin/gram
/usr/bin/ld: cannot find -lboost_random
collect2: error: ld returned 1 exit status
make[2]: *** [bin/gram] Error 1
make[1]: *** [libgramtools/CMakeFiles/gram.dir/all] Error 2`
Installing..Ah, response from sysadmin
If you are building your own boost, which I think you are, then that's your problem! Possibly adding 'random' to the list of libraries in libgramtools/lib/boost.cmake?
ffranr
commented
6 years ago I've just committed work to that effect. Just waiting for it to pass CI tests.
iqbal-lab
commented
6 years ago ooh
ffranr
commented
6 years ago CI tests failed because of too many log messages. But I believe that the solution should work.
iqbal-lab
commented
6 years ago OK, testing...
iqbal-lab
commented
6 years ago Woo - nearly there! Now I think it is assuming I have root
-- [download 100% complete] -- Downloading... done -- extracting... src='/tmp/pip-irixadhf-build/cmake-build-debug/libgramtools/tests/gtest/src/release-1.8.0.zip' dst='/tmp/pip-irixadhf-build/cmake-build-debug/libgramtools/tests/gtest/src/gtest' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done [ 78%] No patch step for 'gtest' [ 79%] No update step for 'gtest' [ 80%] Performing configure step for 'gtest' -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /apps/well/gcc/5.4.0/bin/gcc -- Check for working C compiler: /apps/well/gcc/5.4.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /apps/well/gcc/5.4.0/bin/g++ -- Check for working CXX compiler: /apps/well/gcc/5.4.0/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PythonInterp: /apps/well/python/3.5.2-gcc5.4.0/bin/python (found version "3.5.2") -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Configuring done -- Generating done -- Build files have been written to: /tmp/pip-irixadhf-build/cmake-build-debug/libgramtools/tests/gtest/src/gtest-build [ 82%] Performing build step for 'gtest' Scanning dependencies of target gmock_main [ 9%] Building CXX object googlemock/CMakeFiles/gmock_main.dir/__/googletest/src/gtest-all.cc.o [ 18%] Building CXX object googlemock/CMakeFiles/gmock_main.dir/src/gmock-all.cc.o [ 27%] Building CXX object googlemock/CMakeFiles/gmock_main.dir/src/gmock_main.cc.o [ 36%] Linking CXX static library libgmock_main.a [ 36%] Built target gmock_main Scanning dependencies of target gmock [ 45%] Building CXX object googlemock/CMakeFiles/gmock.dir/__/googletest/src/gtest-all.cc.o [ 54%] Building CXX object googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o [ 63%] Linking CXX static library libgmock.a [ 63%] Built target gmock Scanning dependencies of target gtest [ 72%] Building CXX object googlemock/gtest/CMakeFiles/gtest.dir/src/gtest-all.cc.o [ 81%] Linking CXX static library libgtest.a [ 81%] Built target gtest Scanning dependencies of target gtest_main [ 90%] Building CXX object googlemock/gtest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o [100%] Linking CXX static library libgtest_main.a [100%] Built target gtest_main [ 83%] No install step for 'gtest' [ 84%] Completed 'gtest' [ 84%] Built target gtest Scanning dependencies of target test_main [ 85%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/main.cpp.o [ 87%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/test_search.cpp.o [ 88%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/test_utils.cpp.o [ 89%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/quasimap/coverage/test_common.cpp.o [ 91%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/quasimap/coverage/test_allele_sum.cpp.o [ 92%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/quasimap/coverage/test_allele_base.cpp.o [ 93%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/quasimap/test_quasimap.cpp.o [ 94%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/kmer_index/test_kmers.cpp.o [ 96%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/kmer_index/test_kmer_index.cpp.o [ 97%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/prg/test_prg.cpp.o [ 98%] Building CXX object libgramtools/tests/CMakeFiles/test_main.dir/prg/test_masks.cpp.o [100%] Linking CXX executable test_main [100%] Built target test_main [==========] Running 216 tests from 36 test cases. [----------] Global test environment set-up. [----------] 1 test from LoadAlleleMask [ RUN ] LoadAlleleMask.GivenComplexAlleleMask_SaveAndLoadFromFileCorrectly [ OK ] LoadAlleleMask.GivenComplexAlleleMask_SaveAndLoadFromFileCorrectly (146 ms) [----------] 1 test from LoadAlleleMask (146 ms total)
[----------] 5 tests from GenerateAlleleMask
[ RUN ] GenerateAlleleMask.GivenMultipleSitesAndAlleles_CorrectAlleleMask
[ OK ] GenerateAlleleMask.GivenMultipleSitesAndAlleles_CorrectAlleleMask (139 ms)
[ RUN ] GenerateAlleleMask.SingleVariantSite_CorrectAlleleMask
[ OK ] GenerateAlleleMask.SingleVariantSite_CorrectAlleleMask (158 ms)
[ RUN ] GenerateAlleleMask.SingleVariantSiteThreeAlleles_CorrectAlleleMask
[ OK ] GenerateAlleleMask.SingleVariantSiteThreeAlleles_CorrectAlleleMask (159 ms)
[ RUN ] GenerateAlleleMask.TwoVariantSites_CorrectAlleleMask
[ OK ] GenerateAlleleMask.TwoVariantSites_CorrectAlleleMask (133 ms)
[ RUN ] GenerateAlleleMask.DoubleDigitMarker_CorrectAlleleMask
[ OK ] GenerateAlleleMask.DoubleDigitMarker_CorrectAlleleMask (85 ms)
[----------] 5 tests from GenerateAlleleMask (674 ms total)
[----------] 1 test from GetMaxAlphabetNum
[ RUN ] GetMaxAlphabetNum.GivenPrg_CorrectMaxAlphabetNum
[ OK ] GetMaxAlphabetNum.GivenPrg_CorrectMaxAlphabetNum (57 ms)
[----------] 1 test from GetMaxAlphabetNum (57 ms total)
[----------] 6 tests from GenerateKmerIndex
[ RUN ] GenerateKmerIndex.GivenDataForSingleKmerIndexEntry_CorrectRowDumpGenerated
[ OK ] GenerateKmerIndex.GivenDataForSingleKmerIndexEntry_CorrectRowDumpGenerated (0 ms)
[ RUN ] GenerateKmerIndex.TwoSearchStateOneVairiantPath_CorrectKmerIndexEntryDump
[ OK ] GenerateKmerIndex.TwoSearchStateOneVairiantPath_CorrectKmerIndexEntryDump (0 ms)
[ RUN ] GenerateKmerIndex.GivenVariantSitePaths_DumpVariantSitesPathsCorrectly
[ OK ] GenerateKmerIndex.GivenVariantSitePaths_DumpVariantSitesPathsCorrectly (0 ms)
[ RUN ] GenerateKmerIndex.GivenSaIntervals_DumpSaIntervalsStringCorrectly
[ OK ] GenerateKmerIndex.GivenSaIntervals_DumpSaIntervalsStringCorrectly (0 ms)
[ RUN ] GenerateKmerIndex.GivenKmer_DumpKmerStringCorrectly
[ OK ] GenerateKmerIndex.GivenKmer_DumpKmerStringCorrectly (0 ms)
[ RUN ] GenerateKmerIndex.GivenDnaString_DnaBasesEncodedCorrectly
[ OK ] GenerateKmerIndex.GivenDnaString_DnaBasesEncodedCorrectly (0 ms)
[----------] 6 tests from GenerateKmerIndex (0 ms total)
[----------] 6 tests from ParseKmerIndex
[ RUN ] ParseKmerIndex.GivenKmerIndexEntryStr_CorrectlyParsed
[ OK ] ParseKmerIndex.GivenKmerIndexEntryStr_CorrectlyParsed (0 ms)
[ RUN ] ParseKmerIndex.IndexEntryTwoSearchStatesOneVariantSitePath_ParsedCorrectly
[ OK ] ParseKmerIndex.IndexEntryTwoSearchStatesOneVariantSitePath_ParsedCorrectly (0 ms)
[ RUN ] ParseKmerIndex.GivenEncodedKmerString_CorrectlyParsed
[ OK ] ParseKmerIndex.GivenEncodedKmerString_CorrectlyParsed (0 ms)
[ RUN ] ParseKmerIndex.GivenSaIntervalsString_CorrectlyParsed
[ OK ] ParseKmerIndex.GivenSaIntervalsString_CorrectlyParsed (0 ms)
[ RUN ] ParseKmerIndex.GivenTwoSites_CorrectSiteStructGenerated
[ OK ] ParseKmerIndex.GivenTwoSites_CorrectSiteStructGenerated (0 ms)
[ RUN ] ParseKmerIndex.GivenSitesTrailingAt_TrailingAtIgnored
[ OK ] ParseKmerIndex.GivenSitesTrailingAt_TrailingAtIgnored (0 ms)
[----------] 6 tests from ParseKmerIndex (1 ms total)
[----------] 23 tests from IndexKmers
[ RUN ] IndexKmers.KmerCrossesSecondAllele_CorrectVariantSitePath
Total number of unique kmers: 1
[ OK ] IndexKmers.KmerCrossesSecondAllele_CorrectVariantSitePath (68 ms)
[ RUN ] IndexKmers.KmerCrossesFirstAllele_VariantRegionRecordedInSites
Total number of unique kmers: 1
[ OK ] IndexKmers.KmerCrossesFirstAllele_VariantRegionRecordedInSites (67 ms)
[ RUN ] IndexKmers.BothKmersOverlapVariantSiteAlleles_CorrectSearchResults
Total number of unique kmers: 2
[ OK ] IndexKmers.BothKmersOverlapVariantSiteAlleles_CorrectSearchResults (68 ms)
[ RUN ] IndexKmers.KmerNotFoundInPrg_KmerAbsentFromKmerIndex
Total number of unique kmers: 2
[ OK ] IndexKmers.KmerNotFoundInPrg_KmerAbsentFromKmerIndex (68 ms)
[ RUN ] IndexKmers.OneKmersOverlapsVariantSiteAllele_CorrectSearchResults
Total number of unique kmers: 2
[ OK ] IndexKmers.OneKmersOverlapsVariantSiteAllele_CorrectSearchResults (68 ms)
[ RUN ] IndexKmers.ThreeKmersOverlapSiteThreeAllele_CorrectSearchResults
Total number of unique kmers: 3
[ OK ] IndexKmers.ThreeKmersOverlapSiteThreeAllele_CorrectSearchResults (68 ms)
[ RUN ] IndexKmers.ThreeKmersOneMissMatch_CorrectSearchResults
Total number of unique kmers: 3
[ OK ] IndexKmers.ThreeKmersOneMissMatch_CorrectSearchResults (67 ms)
[ RUN ] IndexKmers.OneKmerStartsAtAllele_SiteFound
Total number of unique kmers: 1
[ OK ] IndexKmers.OneKmerStartsAtAllele_SiteFound (68 ms)
[ RUN ] IndexKmers.KmerFromAlleleCenter_KmerEntryFoundNoVariantSitePath
Total number of unique kmers: 1
[ OK ] IndexKmers.KmerFromAlleleCenter_KmerEntryFoundNoVariantSitePath (57 ms)
[ RUN ] IndexKmers.TwoKmersStartAtAllele_SitesFound
Total number of unique kmers: 2
[ OK ] IndexKmers.TwoKmersStartAtAllele_SitesFound (68 ms)
[ RUN ] IndexKmers.KmerEndingInAllele_SingleSiteFound
Total number of unique kmers: 1
[ OK ] IndexKmers.KmerEndingInAllele_SingleSiteFound (68 ms)
[ RUN ] IndexKmers.TwoKmersEndingInAlleles_TwoSingleSitesFound
Total number of unique kmers: 2
[ OK ] IndexKmers.TwoKmersEndingInAlleles_TwoSingleSitesFound (68 ms)
[ RUN ] IndexKmers.KmerStartingInSiteAndEndInAnotherSite_CorrectVariantSitePath
Total number of unique kmers: 1
[ OK ] IndexKmers.KmerStartingInSiteAndEndInAnotherSite_CorrectVariantSitePath (56 ms)
[ RUN ] IndexKmers.TwoSearchStatesIdenticalSaIntervals_DifferentVariantSitePaths
Total number of unique kmers: 1
[ OK ] IndexKmers.TwoSearchStatesIdenticalSaIntervals_DifferentVariantSitePaths (68 ms)
[ RUN ] IndexKmers.GivenPrgWithLongNonVariantTail_KmerEndingAtTailExtracted
Total number of unique kmers: 107
[ OK ] IndexKmers.GivenPrgWithLongNonVariantTail_KmerEndingAtTailExtracted (45 ms)
[ RUN ] IndexKmers.GivenPrgWithLongNonVariantTail_KmerStartingAtLeftMostAlleleCharExtracted
Total number of unique kmers: 107
[ OK ] IndexKmers.GivenPrgWithLongNonVariantTail_KmerStartingAtLeftMostAlleleCharExtracted (45 ms)
[ RUN ] IndexKmers.GivenPrgWithLongNonVariantTail_KmerImmediatelyAfterSiteExtracted
Total number of unique kmers: 107
[ OK ] IndexKmers.GivenPrgWithLongNonVariantTail_KmerImmediatelyAfterSiteExtracted (44 ms)
[ RUN ] IndexKmers.KmerStartsOneBaseBeyondRangeEdge_KmerNotExtracted
Total number of unique kmers: 107
[ OK ] IndexKmers.KmerStartsOneBaseBeyondRangeEdge_KmerNotExtracted (45 ms)
[ RUN ] IndexKmers.KmerStartsAtRangeEdge_KmerExtracted
Total number of unique kmers: 108
[ OK ] IndexKmers.KmerStartsAtRangeEdge_KmerExtracted (44 ms)
[ RUN ] IndexKmers.KmerWithinMaxReadSizeRegionNoSiteOverlap_KmerFound
Total number of unique kmers: 14
[ OK ] IndexKmers.KmerWithinMaxReadSizeRegionNoSiteOverlap_KmerFound (50 ms)
[ RUN ] IndexKmers.KmerEndJustOutsideMaxReadSize_KmerNotFoundInIndex
Total number of unique kmers: 13
[ OK ] IndexKmers.KmerEndJustOutsideMaxReadSize_KmerNotFoundInIndex (51 ms)
[ RUN ] IndexKmers.TwoSitesAndKmerWithinMaxReadSizeRegionNoSiteOverlap_KmerFound
Total number of unique kmers: 17
[ OK ] IndexKmers.TwoSitesAndKmerWithinMaxReadSizeRegionNoSiteOverlap_KmerFound (51 ms)
[ RUN ] IndexKmers.TwoSitesAndKmerOutsideMaxReadSizeRegionNoSiteOverlap_KmerNotFound
Total number of unique kmers: 16
[ OK ] IndexKmers.TwoSitesAndKmerOutsideMaxReadSizeRegionNoSiteOverlap_KmerNotFound (50 ms)
[----------] 23 tests from IndexKmers (1353 ms total)
[----------] 3 tests from GetBoundaryMarkerIndexes
[ RUN ] GetBoundaryMarkerIndexes.TwoVariantSites_CorrectSiteStartEndIndexes
[ OK ] GetBoundaryMarkerIndexes.TwoVariantSites_CorrectSiteStartEndIndexes (57 ms)
[ RUN ] GetBoundaryMarkerIndexes.OneVariantSites_CorrectSiteStartEndIndexes
[ OK ] GetBoundaryMarkerIndexes.OneVariantSites_CorrectSiteStartEndIndexes (68 ms)
[ RUN ] GetBoundaryMarkerIndexes.NoVariantSites_NoSiteIndexes
[ OK ] GetBoundaryMarkerIndexes.NoVariantSites_NoSiteIndexes (68 ms)
[----------] 3 tests from GetBoundaryMarkerIndexes (193 ms total)
[----------] 4 tests from GetKmerRegionRange
[ RUN ] GetKmerRegionRange.VariantSiteCloseToStart_CorrectKmerRegionEndIndexes
[ OK ] GetKmerRegionRange.VariantSiteCloseToStart_CorrectKmerRegionEndIndexes (67 ms)
[ RUN ] GetKmerRegionRange.VariantSiteCloseToEnd_CorrectKmerRegionEndIndexes
[ OK ] GetKmerRegionRange.VariantSiteCloseToEnd_CorrectKmerRegionEndIndexes (57 ms)
[ RUN ] GetKmerRegionRange.TwoVariantSites_FirstKmerRegionExtendedToBoundaryEndOfSecond
[ OK ] GetKmerRegionRange.TwoVariantSites_FirstKmerRegionExtendedToBoundaryEndOfSecond (57 ms)
[ RUN ] GetKmerRegionRange.GivenMaxReadSizeOne_RangeEndAtSiteBoundaryEnd
[ OK ] GetKmerRegionRange.GivenMaxReadSizeOne_RangeEndAtSiteBoundaryEnd (68 ms)
[----------] 4 tests from GetKmerRegionRange (249 ms total)
[----------] 7 tests from FindSiteEndBoundary
[ RUN ] FindSiteEndBoundary.GivenAlleleIndex_ReturnSiteEndMarkerIndex
[ OK ] FindSiteEndBoundary.GivenAlleleIndex_ReturnSiteEndMarkerIndex (67 ms)
[ RUN ] FindSiteEndBoundary.GivenAlleleIndexAndSiteEndingPrg_ReturnSiteEndMarkerIndex
[ OK ] FindSiteEndBoundary.GivenAlleleIndexAndSiteEndingPrg_ReturnSiteEndMarkerIndex (68 ms)
[ RUN ] FindSiteEndBoundary.GivenMultiCharAllele_ReturnSiteEndMarkerIndex
[ OK ] FindSiteEndBoundary.GivenMultiCharAllele_ReturnSiteEndMarkerIndex (68 ms)
[ RUN ] FindSiteEndBoundary.GivenAlleleMarkerIndex_ReturnSiteEndMarkerIndex
[ OK ] FindSiteEndBoundary.GivenAlleleMarkerIndex_ReturnSiteEndMarkerIndex (68 ms)
[ RUN ] FindSiteEndBoundary.GivenStartBoundaryMarkerIndex_ReturnEndBoundaryMarkerIndex
[ OK ] FindSiteEndBoundary.GivenStartBoundaryMarkerIndex_ReturnEndBoundaryMarkerIndex (68 ms)
[ RUN ] FindSiteEndBoundary.GivenSiteEndingAtPrgEnd_ReturnCorrectEndBoundaryMarkerIndex
[ OK ] FindSiteEndBoundary.GivenSiteEndingAtPrgEnd_ReturnCorrectEndBoundaryMarkerIndex (67 ms)
[ RUN ] FindSiteEndBoundary.GivenEndBoundaryMarkerIndex_ReturnEndBoundaryMarkerIndex
[ OK ] FindSiteEndBoundary.GivenEndBoundaryMarkerIndex_ReturnEndBoundaryMarkerIndex (68 ms)
[----------] 7 tests from FindSiteEndBoundary (474 ms total)
[----------] 4 tests from GetSiteOrderedAlleles
[ RUN ] GetSiteOrderedAlleles.GivenSiteWithMultiCharAlleles_CorrectAllelesExtracted
[ OK ] GetSiteOrderedAlleles.GivenSiteWithMultiCharAlleles_CorrectAllelesExtracted (67 ms)
[ RUN ] GetSiteOrderedAlleles.GivenBondaryEndMarkerIndex_CorrectAllelesExtracted
[ OK ] GetSiteOrderedAlleles.GivenBondaryEndMarkerIndex_CorrectAllelesExtracted (68 ms)
[ RUN ] GetSiteOrderedAlleles.GivenSiteWithSingleCharAllele_CorrectAllelesExtracted
[ OK ] GetSiteOrderedAlleles.GivenSiteWithSingleCharAllele_CorrectAllelesExtracted (68 ms)
[ RUN ] GetSiteOrderedAlleles.GivenSiteWithThreeAlleles_CorrectAllelesExtracted
[ OK ] GetSiteOrderedAlleles.GivenSiteWithThreeAlleles_CorrectAllelesExtracted (67 ms)
[----------] 4 tests from GetSiteOrderedAlleles (270 ms total)
[----------] 10 tests from InrangeLeftSites
[ RUN ] InrangeLeftSites.NoSitesWithinRange_NoSiteEndIndexesReturned
[ OK ] InrangeLeftSites.NoSitesWithinRange_NoSiteEndIndexesReturned (68 ms)
[ RUN ] InrangeLeftSites.SiteOutsideKmerSize_NoSiteEndIndexesReturned
[ OK ] InrangeLeftSites.SiteOutsideKmerSize_NoSiteEndIndexesReturned (67 ms)
[ RUN ] InrangeLeftSites.SiteStartIndexAtBoundaryEnd_SiteRecognizeBoundaryIndexReturned
[ OK ] InrangeLeftSites.SiteStartIndexAtBoundaryEnd_SiteRecognizeBoundaryIndexReturned (68 ms)
[ RUN ] InrangeLeftSites.SiteJustInsideKmerSize_SiteEndIndexReturned
[ OK ] InrangeLeftSites.SiteJustInsideKmerSize_SiteEndIndexReturned (67 ms)
[ RUN ] InrangeLeftSites.KmerExtendsToFirstSiteMarker_SiteEndIndexReturned
[ OK ] InrangeLeftSites.KmerExtendsToFirstSiteMarker_SiteEndIndexReturned (68 ms)
[ RUN ] InrangeLeftSites.KmerExtendsBeyondSite_SiteEndIndexReturned
[ OK ] InrangeLeftSites.KmerExtendsBeyondSite_SiteEndIndexReturned (68 ms)
[ RUN ] InrangeLeftSites.KmerCoversMultipleSites_SiteEndIndexesReturned
[ OK ] InrangeLeftSites.KmerCoversMultipleSites_SiteEndIndexesReturned (56 ms)
[ RUN ] InrangeLeftSites.KmerCoverageEndsBeforeFirstSite_OnlySecondSiteEndIndexReturned
[ OK ] InrangeLeftSites.KmerCoverageEndsBeforeFirstSite_OnlySecondSiteEndIndexReturned (57 ms)
[ RUN ] InrangeLeftSites.KmerCoverageExtendsJustWithinFirstSite_SiteEndIndexesReturned
[ OK ] InrangeLeftSites.KmerCoverageExtendsJustWithinFirstSite_SiteEndIndexesReturned (57 ms)
[ RUN ] InrangeLeftSites.SecondSiteAlleleLengthsNotLimitKmerCoverage_BothSiteEndIndexesReturned
[ OK ] InrangeLeftSites.SecondSiteAlleleLengthsNotLimitKmerCoverage_BothSiteEndIndexesReturned (57 ms)
[----------] 10 tests from InrangeLeftSites (633 ms total)
[----------] 4 tests from GetNonvariantRegion
[ RUN ] GetNonvariantRegion.GivenFirstSiteEndBoundaryIndex_ReturnRegionInclusiveRange
[ OK ] GetNonvariantRegion.GivenFirstSiteEndBoundaryIndex_ReturnRegionInclusiveRange (57 ms)
[ RUN ] GetNonvariantRegion.GivenLastSiteEndBoundaryIndex_ReturnRegionInclusiveRange
[ OK ] GetNonvariantRegion.GivenLastSiteEndBoundaryIndex_ReturnRegionInclusiveRange (56 ms)
[ RUN ] GetNonvariantRegion.GivenSiteEndBoundaryIndexEndingPrg_ReturnZeroRange
[ OK ] GetNonvariantRegion.GivenSiteEndBoundaryIndexEndingPrg_ReturnZeroRange (69 ms)
[ RUN ] GetNonvariantRegion.GivenSiteEndBoundaryIndexJustBeforePrgEnd_ReturnRegionInclusiveRange
[ OK ] GetNonvariantRegion.GivenSiteEndBoundaryIndexJustBeforePrgEnd_ReturnRegionInclusiveRange (68 ms)
[----------] 4 tests from GetNonvariantRegion (250 ms total)
[----------] 4 tests from ExtractRightNonvariantRegion
[ RUN ] ExtractRightNonvariantRegion.GivenSiteEndBoundaryIndexBeforePrgEnd_CorrectNonvariantRegion
[ OK ] ExtractRightNonvariantRegion.GivenSiteEndBoundaryIndexBeforePrgEnd_CorrectNonvariantRegion (68 ms)
[ RUN ] ExtractRightNonvariantRegion.GivenSiteEndBoundaryIndexJustBeforePrgEnd_CorrectNonvariantRegion
[ OK ] ExtractRightNonvariantRegion.GivenSiteEndBoundaryIndexJustBeforePrgEnd_CorrectNonvariantRegion (67 ms)
[ RUN ] ExtractRightNonvariantRegion.GivenSiteEndBoundaryIndexBeforeSecondSite_CorrectNonvariantRegion
[ OK ] ExtractRightNonvariantRegion.GivenSiteEndBoundaryIndexBeforeSecondSite_CorrectNonvariantRegion (57 ms)
[ RUN ] ExtractRightNonvariantRegion.GivenSingleBaseNonvariantRegion_CorrectNonvariantRegion
[ OK ] ExtractRightNonvariantRegion.GivenSingleBaseNonvariantRegion_CorrectNonvariantRegion (57 ms)
[----------] 4 tests from ExtractRightNonvariantRegion (249 ms total)
[----------] 5 tests from GetReverseKmersFromRegion
[ RUN ] GetReverseKmersFromRegion.NoVariantSite_CorrectReverseKmers
[ OK ] GetReverseKmersFromRegion.NoVariantSite_CorrectReverseKmers (68 ms)
[ RUN ] GetReverseKmersFromRegion.KmerSizeKmerRangeStartsAtIndexZero_CorrectReverseKmer
[ OK ] GetReverseKmersFromRegion.KmerSizeKmerRangeStartsAtIndexZero_CorrectReverseKmer (67 ms)
[ RUN ] GetReverseKmersFromRegion.NoVariantSite_FourCorrectReverseKmersFromPrgEnd
[ OK ] GetReverseKmersFromRegion.NoVariantSite_FourCorrectReverseKmersFromPrgEnd (68 ms)
[ RUN ] GetReverseKmersFromRegion.GivenKmerRegionRange_CorrectReverseKmers
[ OK ] GetReverseKmersFromRegion.GivenKmerRegionRange_CorrectReverseKmers (68 ms)
[ RUN ] GetReverseKmersFromRegion.GivenKmerRegion_CorrectReverseKmerFound
[ OK ] GetReverseKmersFromRegion.GivenKmerRegion_CorrectReverseKmerFound (50 ms)
[----------] 5 tests from GetReverseKmersFromRegion (321 ms total)
[----------] 1 test from FindSiteStartBoundary
[ RUN ] FindSiteStartBoundary.GivenSiteEndIndex_CorrectSiteStartIndex
[ OK ] FindSiteStartBoundary.GivenSiteEndIndex_CorrectSiteStartIndex (57 ms)
[----------] 1 test from FindSiteStartBoundary (57 ms total)
[----------] 4 tests from GetKmerSizeRegionParts
[ RUN ] GetKmerSizeRegionParts.TwoSitesInRange_CorrectRegionParts
[ OK ] GetKmerSizeRegionParts.TwoSitesInRange_CorrectRegionParts (56 ms)
[ RUN ] GetKmerSizeRegionParts.NonVariantTailAfterLastSite_TailIncludedAsRegionPart
[ OK ] GetKmerSizeRegionParts.NonVariantTailAfterLastSite_TailIncludedAsRegionPart (57 ms)
[ RUN ] GetKmerSizeRegionParts.TwoSitesInRangeEndRegionAtSiteEnd_CorrectRegionParts
[ OK ] GetKmerSizeRegionParts.TwoSitesInRangeEndRegionAtSiteEnd_CorrectRegionParts (54 ms)
[ RUN ] GetKmerSizeRegionParts.TwoSitesInRangeSingleCharAfterSiteEnd_CorrectRegionParts
[ OK ] GetKmerSizeRegionParts.TwoSitesInRangeSingleCharAfterSiteEnd_CorrectRegionParts (54 ms)
[----------] 4 tests from GetKmerSizeRegionParts (221 ms total)
[----------] 6 tests from UpdateAlleleIndePath
[ RUN ] UpdateAlleleIndePath.GivenAllZerosAlleleIndexPath_LastIndexIncremented
[ OK ] UpdateAlleleIndePath.GivenAllZerosAlleleIndexPath_LastIndexIncremented (0 ms)
[ RUN ] UpdateAlleleIndePath.GivenAlleleIndexPath_FirstIndexIncremented
[ OK ] UpdateAlleleIndePath.GivenAlleleIndexPath_FirstIndexIncremented (0 ms)
[ RUN ] UpdateAlleleIndePath.GivenAlleleIndexPath_LastIndexIncremented
[ OK ] UpdateAlleleIndePath.GivenAlleleIndexPath_LastIndexIncremented (0 ms)
[ RUN ] UpdateAlleleIndePath.ThreeAllelesInLastPlace_LastIndexIncremented
[ OK ] UpdateAlleleIndePath.ThreeAllelesInLastPlace_LastIndexIncremented (0 ms)
[ RUN ] UpdateAlleleIndePath.ThreeAllelesInMidPlace_MidIndexIncremented
[ OK ] UpdateAlleleIndePath.ThreeAllelesInMidPlace_MidIndexIncremented (0 ms)
[ RUN ] UpdateAlleleIndePath.CantUpdateFurther_ReturnFalse
[ OK ] UpdateAlleleIndePath.CantUpdateFurther_ReturnFalse (0 ms)
[----------] 6 tests from UpdateAlleleIndePath (0 ms total)
[----------] 6 tests from GetPathsFromParts
[ RUN ] GetPathsFromParts.GivenKmerSizeRegionParts_CorrectPaths
[ OK ] GetPathsFromParts.GivenKmerSizeRegionParts_CorrectPaths (0 ms)
[ RUN ] GetPathsFromParts.GivenThreeCharAlleleInLastRegion_CorrectPaths
[ OK ] GetPathsFromParts.GivenThreeCharAlleleInLastRegion_CorrectPaths (0 ms)
[ RUN ] GetPathsFromParts.MidRegionContainsTwoAlleles_CorrectPaths
[ OK ] GetPathsFromParts.MidRegionContainsTwoAlleles_CorrectPaths (0 ms)
[ RUN ] GetPathsFromParts.MidRegionContainsThreeAlleles_CorrectPaths
[ OK ] GetPathsFromParts.MidRegionContainsThreeAlleles_CorrectPaths (0 ms)
[ RUN ] GetPathsFromParts.SingleRegionWithSingleCharAllele_CorrectPath
[ OK ] GetPathsFromParts.SingleRegionWithSingleCharAllele_CorrectPath (0 ms)
[ RUN ] GetPathsFromParts.GivenPrgAndSinglePath_CorrectPathExtractedFromPrg
[ OK ] GetPathsFromParts.GivenPrgAndSinglePath_CorrectPathExtractedFromPrg (47 ms)
[----------] 6 tests from GetPathsFromParts (47 ms total)
[----------] 4 tests from GetReverseKmersFromPath
[ RUN ] GetReverseKmersFromPath.GivenPath_CorrectReverseKmers
[ OK ] GetReverseKmersFromPath.GivenPath_CorrectReverseKmers (0 ms)
[ RUN ] GetReverseKmersFromPath.GivenTooShortPath_NoKmers
[ OK ] GetReverseKmersFromPath.GivenTooShortPath_NoKmers (0 ms)
[ RUN ] GetReverseKmersFromPath.GivenKmerSizePath_CorrectReverseKmer
[ OK ] GetReverseKmersFromPath.GivenKmerSizePath_CorrectReverseKmer (0 ms)
[ RUN ] GetReverseKmersFromPath.GivenPath_CorrectReverseKmerExtracted
[ OK ] GetReverseKmersFromPath.GivenPath_CorrectReverseKmerExtracted (0 ms)
[----------] 4 tests from GetReverseKmersFromPath (0 ms total)
[----------] 10 tests from ExtractVariantReverseKmers
[ RUN ] ExtractVariantReverseKmers.GivenInrangeSite_CorrectReverseKmers
[ OK ] ExtractVariantReverseKmers.GivenInrangeSite_CorrectReverseKmers (63 ms)
[ RUN ] ExtractVariantReverseKmers.SingleSiteInRange_CorrectReverseKmers
[ OK ] ExtractVariantReverseKmers.SingleSiteInRange_CorrectReverseKmers (64 ms)
[ RUN ] ExtractVariantReverseKmers.SiteStartsAtPrgStart_CorrectReverseKmers
[ OK ] ExtractVariantReverseKmers.SiteStartsAtPrgStart_CorrectReverseKmers (63 ms)
[ RUN ] ExtractVariantReverseKmers.SiteEndsAtPrgEnd_CorrectReverseKmers
[ OK ] ExtractVariantReverseKmers.SiteEndsAtPrgEnd_CorrectReverseKmers (64 ms)
[ RUN ] ExtractVariantReverseKmers.SingleSiteMultiCharAllele_CorrectReverseKmers
[ OK ] ExtractVariantReverseKmers.SingleSiteMultiCharAllele_CorrectReverseKmers (64 ms)
[ RUN ] ExtractVariantReverseKmers.TwoSitesNoCrossingKmers_CorrectReverseKmers
[ OK ] ExtractVariantReverseKmers.TwoSitesNoCrossingKmers_CorrectReverseKmers (64 ms)
[ RUN ] ExtractVariantReverseKmers.TwoSitesWithCrossingKmers_CorrectReverseKmers
[ OK ] ExtractVariantReverseKmers.TwoSitesWithCrossingKmers_CorrectReverseKmers (63 ms)
[ RUN ] ExtractVariantReverseKmers.SingleSiteSingleKmerFromAllele_CorrectReverseKmer
[ OK ] ExtractVariantReverseKmers.SingleSiteSingleKmerFromAllele_CorrectReverseKmer (64 ms)
[ RUN ] ExtractVariantReverseKmers.SingleSiteTwoKmersFromAllele_CorrectReverseKmer
[ OK ] ExtractVariantReverseKmers.SingleSiteTwoKmersFromAllele_CorrectReverseKmer (64 ms)
[ RUN ] ExtractVariantReverseKmers.GivenInrangeSite_CorrectNewCurrentIndex
[ OK ] ExtractVariantReverseKmers.GivenInrangeSite_CorrectNewCurrentIndex (63 ms)
[----------] 10 tests from ExtractVariantReverseKmers (636 ms total)
[----------] 6 tests from CombineOverlappingRegions
[ RUN ] CombineOverlappingRegions.SetOfRangesAllEncapsulatedWithinFirstRange_CorrectSingleRange
[ OK ] CombineOverlappingRegions.SetOfRangesAllEncapsulatedWithinFirstRange_CorrectSingleRange (0 ms)
[ RUN ] CombineOverlappingRegions.ExactlyTwoNonOverlappingRanges_CorrectTwoRanges
[ OK ] CombineOverlappingRegions.ExactlyTwoNonOverlappingRanges_CorrectTwoRanges (0 ms)
[ RUN ] CombineOverlappingRegions.TwoRangesEqualEndStart_CorrectRange
[ OK ] CombineOverlappingRegions.TwoRangesEqualEndStart_CorrectRange (0 ms)
[ RUN ] CombineOverlappingRegions.StartOfSecondInMidOfFirst_SingleRange
[ OK ] CombineOverlappingRegions.StartOfSecondInMidOfFirst_SingleRange (0 ms)
[ RUN ] CombineOverlappingRegions.CommonStart_SingleRegionWithLargestEnd
[ OK ] CombineOverlappingRegions.CommonStart_SingleRegionWithLargestEnd (0 ms)
[ RUN ] CombineOverlappingRegions.EmptyRange_EmptyRange
[ OK ] CombineOverlappingRegions.EmptyRange_EmptyRange (0 ms)
[----------] 6 tests from CombineOverlappingRegions (0 ms total)
[----------] 3 tests from GetReversedKmers
[ RUN ] GetReversedKmers.GivenRandomlyArrangedReverseKmers_KmersReversedAndSortedByRightMostBase
[ OK ] GetReversedKmers.GivenRandomlyArrangedReverseKmers_KmersReversedAndSortedByRightMostBase (0 ms)
[ RUN ] GetReversedKmers.GivenSingleReverseKmer_CorrectReversedKmer
[ OK ] GetReversedKmers.GivenSingleReverseKmer_CorrectReversedKmer (0 ms)
[ RUN ] GetReversedKmers.SortingReverseKmerFromRightToLeft_CorrectReversedKmers
[ OK ] GetReversedKmers.SortingReverseKmerFromRightToLeft_CorrectReversedKmers (0 ms)
[----------] 3 tests from GetReversedKmers (0 ms total)
[----------] 3 tests from GetPrefixDiffs
[ RUN ] GetPrefixDiffs.GivenKmersDifferInLeftMostBaseOnly_CorrectPrefixDiffs
[ OK ] GetPrefixDiffs.GivenKmersDifferInLeftMostBaseOnly_CorrectPrefixDiffs (0 ms)
[ RUN ] GetPrefixDiffs.GivenKmerDifferInRightMostBaseOnly_CorrectPrefixDiffs
[ OK ] GetPrefixDiffs.GivenKmerDifferInRightMostBaseOnly_CorrectPrefixDiffs (0 ms)
[ RUN ] GetPrefixDiffs.GivenMixOfOrderedKmers_CorrectPrefixDiffs
[ OK ] GetPrefixDiffs.GivenMixOfOrderedKmers_CorrectPrefixDiffs (0 ms)
[----------] 3 tests from GetPrefixDiffs (0 ms total)
[----------] 8 tests from GetAllReverseKmers
[ RUN ] GetAllReverseKmers.GivenOverkillMaxReadSize_AllPossibleKmersReturned
[ OK ] GetAllReverseKmers.GivenOverkillMaxReadSize_AllPossibleKmersReturned (63 ms)
[ RUN ] GetAllReverseKmers.KmerPossibleAfterVariantSite_ReverseKmerIncludedInResult
[ OK ] GetAllReverseKmers.KmerPossibleAfterVariantSite_ReverseKmerIncludedInResult (64 ms)
[ RUN ] GetAllReverseKmers.SecondVariantSiteEndsAtPrgEnd_CorrectReverseKmers
[ OK ] GetAllReverseKmers.SecondVariantSiteEndsAtPrgEnd_CorrectReverseKmers (53 ms)
[ RUN ] GetAllReverseKmers.KmersOverlappingTwoVariantSites_CorrectReverseKmers
[ OK ] GetAllReverseKmers.KmersOverlappingTwoVariantSites_CorrectReverseKmers (54 ms)
[ RUN ] GetAllReverseKmers.TwoLeftMostKmersWithinRange_TwoLeftMostKmersIncluded
[ OK ] GetAllReverseKmers.TwoLeftMostKmersWithinRange_TwoLeftMostKmersIncluded (65 ms)
[ RUN ] GetAllReverseKmers.MaxReadSizeLessThanKmerSize_AlleleKmersReturned
[ OK ] GetAllReverseKmers.MaxReadSizeLessThanKmerSize_AlleleKmersReturned (64 ms)
[ RUN ] GetAllReverseKmers.GivenPrg_CorrectReverseKmerFound
[ OK ] GetAllReverseKmers.GivenPrg_CorrectReverseKmerFound (47 ms)
[ RUN ] GetAllReverseKmers.GivenPrgWithLongNonVariantTail_PreviouslyAbsentKmerFound
[ OK ] GetAllReverseKmers.GivenPrgWithLongNonVariantTail_PreviouslyAbsentKmerFound (49 ms)
[----------] 8 tests from GetAllReverseKmers (459 ms total)
[----------] 1 test from GetAllOrderedKmers
[ RUN ] GetAllOrderedKmers.GivenPrg_CorrectForwardKmerFound
[ OK ] GetAllOrderedKmers.GivenPrg_CorrectForwardKmerFound (49 ms)
[----------] 1 test from GetAllOrderedKmers (49 ms total)
[----------] 1 test from GetKmerPrefixDiffs
[ RUN ] GetKmerPrefixDiffs.GivenPrgAndTargetKmer_CorrespondingPrefixDiffEntryFound
[ OK ] GetKmerPrefixDiffs.GivenPrgAndTargetKmer_CorrespondingPrefixDiffEntryFound (51 ms)
[----------] 1 test from GetKmerPrefixDiffs (51 ms total)
[----------] 16 tests from Quasimap
[ RUN ] Quasimap.GivenReadAndKmerSize_CorrectKmerReturned
[ OK ] Quasimap.GivenReadAndKmerSize_CorrectKmerReturned (0 ms)
[ RUN ] Quasimap.ReadCrossingSecondVariantSecondAllele_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.ReadCrossingSecondVariantSecondAllele_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.ReadCrossingSecondVariantFirstAllele_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.ReadCrossingSecondVariantFirstAllele_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.ReadCrossingMultipleVariantSites_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.ReadCrossingMultipleVariantSites_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.ReadCrossingMultipleVariantSitesEndingInAllele_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.ReadCrossingMultipleVariantSitesEndingInAllele_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.NonMappingReadCrossingAllele_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.NonMappingReadCrossingAllele_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.ReadEndsInAllele_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.ReadEndsInAllele_CorrectAlleleCoverage (58 ms)
[ RUN ] Quasimap.ReadStartsInAllele_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.ReadStartsInAllele_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.ReadWithNoMatchingKmer_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.ReadWithNoMatchingKmer_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.ReadMapsToThreePositions_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.ReadMapsToThreePositions_CorrectAlleleCoverage (56 ms)
[ RUN ] Quasimap.ReadEntierlyWithinAllele_CoverageNotRecorded
Total number of unique kmers: 1
[ OK ] Quasimap.ReadEntierlyWithinAllele_CoverageNotRecorded (56 ms)
[ RUN ] Quasimap.MappingMultipleIdenticalReads_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.MappingMultipleIdenticalReads_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.MappingTwoReadsIdenticalKmers_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.MappingTwoReadsIdenticalKmers_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.MappingThreeReadsIdenticalKmers_CorrectAlleleCoverage
Total number of unique kmers: 1
[ OK ] Quasimap.MappingThreeReadsIdenticalKmers_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.MappingThreeReadsDifferentKmers_CorrectAlleleCoverage
Total number of unique kmers: 2
[ OK ] Quasimap.MappingThreeReadsDifferentKmers_CorrectAlleleCoverage (57 ms)
[ RUN ] Quasimap.MappingThreeReadsOneReadMappsTwice_CorrectAlleleCoverage
Total number of unique kmers: 2
[ OK ] Quasimap.MappingThreeReadsOneReadMappsTwice_CorrectAlleleCoverage (57 ms)
[----------] 16 tests from Quasimap (855 ms total)
[----------] 12 tests from AlleleBaseCoverage
[ RUN ] AlleleBaseCoverage.ReadCoversTwoSites_CorrectAlleleBaseCoverage
[ OK ] AlleleBaseCoverage.ReadCoversTwoSites_CorrectAlleleBaseCoverage (57 ms)
[ RUN ] AlleleBaseCoverage.ShortReadStartingOutsideSiteCoversTwoSites_FinishesBeforeSecondAlleleEnd
[ OK ] AlleleBaseCoverage.ShortReadStartingOutsideSiteCoversTwoSites_FinishesBeforeSecondAlleleEnd (57 ms)
[ RUN ] AlleleBaseCoverage.ReadStartsWithinOneAlleleFinishesBeforeEndOfSecond_CorrectCoverage
[ OK ] AlleleBaseCoverage.ReadStartsWithinOneAlleleFinishesBeforeEndOfSecond_CorrectCoverage (57 ms)
[ RUN ] AlleleBaseCoverage.GivenTwoSites_CorrectInterSiteBaseCount
[ OK ] AlleleBaseCoverage.GivenTwoSites_CorrectInterSiteBaseCount (57 ms)
[ RUN ] AlleleBaseCoverage.SaIntervalGreaterThanOne_CorrectCumulativeBaseCoverage
[ OK ] AlleleBaseCoverage.SaIntervalGreaterThanOne_CorrectCumulativeBaseCoverage (67 ms)
[ RUN ] AlleleBaseCoverage.ReadStartsBeforeSiteCoversFirstAllele_CorrectBaseCoverage
[ OK ] AlleleBaseCoverage.ReadStartsBeforeSiteCoversFirstAllele_CorrectBaseCoverage (68 ms)
[ RUN ] AlleleBaseCoverage.ReadStartsWithinFirstAllele_OnlyLastAlleleBaseCovered
[ OK ] AlleleBaseCoverage.ReadStartsWithinFirstAllele_OnlyLastAlleleBaseCovered (68 ms)
[ RUN ] AlleleBaseCoverage.ReadStartsWithinSecondAllele_PartialAlleleBaseCoverage
[ OK ] AlleleBaseCoverage.ReadStartsWithinSecondAllele_PartialAlleleBaseCoverage (67 ms)
[ RUN ] AlleleBaseCoverage.ReadStartsOutsideSiteEndsBeforeAlleleEnd_PartialCoverageOfAllele
[ OK ] AlleleBaseCoverage.ReadStartsOutsideSiteEndsBeforeAlleleEnd_PartialCoverageOfAllele (68 ms)
[ RUN ] AlleleBaseCoverage.GivenSiteStartingAtPrgStart_CorrectAlleleBaseCoverageStructure
[ OK ] AlleleBaseCoverage.GivenSiteStartingAtPrgStart_CorrectAlleleBaseCoverageStructure (68 ms)
[ RUN ] AlleleBaseCoverage.GivenOneVariantSite_CorrectAlleleBaseCoverageStructure
[ OK ] AlleleBaseCoverage.GivenOneVariantSite_CorrectAlleleBaseCoverageStructure (67 ms)
[ RUN ] AlleleBaseCoverage.GivenTwoVariantSites_CorrectAlleleBaseCoverageStructure
[ OK ] AlleleBaseCoverage.GivenTwoVariantSites_CorrectAlleleBaseCoverageStructure (57 ms)
[----------] 12 tests from AlleleBaseCoverage (758 ms total)
[----------] 3 tests from AlleleSumCoverage
[ RUN ] AlleleSumCoverage.GivenOneVariantSite_CorrectAlleleSumCoverageStructure
[ OK ] AlleleSumCoverage.GivenOneVariantSite_CorrectAlleleSumCoverageStructure (57 ms)
[ RUN ] AlleleSumCoverage.GivenTwoVariantSite_CorrectAlleleSumCoverageStructure
[ OK ] AlleleSumCoverage.GivenTwoVariantSite_CorrectAlleleSumCoverageStructure (57 ms)
[ RUN ] AlleleSumCoverage.GivenThreeVariantSites_CorrectAlleleSumCoverageStructure
[ OK ] AlleleSumCoverage.GivenThreeVariantSites_CorrectAlleleSumCoverageStructure (57 ms)
[----------] 3 tests from AlleleSumCoverage (171 ms total)
[----------] 2 tests from CoverageCommon
[ RUN ] CoverageCommon.GivenSearchStatesAndFixedSeed_CorrectRandomlySelectedSaInterval
[ OK ] CoverageCommon.GivenSearchStatesAndFixedSeed_CorrectRandomlySelectedSaInterval (0 ms)
[ RUN ] CoverageCommon.GivenTargetSaInterval_ReturnOnlySearchStatesWithTarget
[ OK ] CoverageCommon.GivenTargetSaInterval_ReturnOnlySearchStatesWithTarget (0 ms)
[----------] 2 tests from CoverageCommon (0 ms total)
[----------] 2 tests from GenerateSitesMask
[ RUN ] GenerateSitesMask.SingleVariantSiteTwoAlleles_CorrectSitesMask
[ OK ] GenerateSitesMask.SingleVariantSiteTwoAlleles_CorrectSitesMask (0 ms)
[ RUN ] GenerateSitesMask.TwoVariantSites_CorrectSitesMask
[ OK ] GenerateSitesMask.TwoVariantSites_CorrectSitesMask (0 ms)
[----------] 2 tests from GenerateSitesMask (0 ms total)
[----------] 2 tests from MaxAlphabetNum
[ RUN ] MaxAlphabetNum.PrgWithVariantSite_LargestSiteMarkerAsMaxAlphabet
[ OK ] MaxAlphabetNum.PrgWithVariantSite_LargestSiteMarkerAsMaxAlphabet (0 ms)
[ RUN ] MaxAlphabetNum.SingleCharPrg_CorrectBaseEncodingAsMaxAlphabet
[ OK ] MaxAlphabetNum.SingleCharPrg_CorrectBaseEncodingAsMaxAlphabet (0 ms)
[----------] 2 tests from MaxAlphabetNum (0 ms total)
[----------] 1 test from ReverseComplimentRead
[ RUN ] ReverseComplimentRead.GivenRead_ReverseComplimnetReadReturned
[ OK ] ReverseComplimentRead.GivenRead_ReverseComplimnetReadReturned (0 ms)
[----------] 1 test from ReverseComplimentRead (0 ms total)
[----------] 38 tests from Search
[ RUN ] Search.SingleChar_CorrectSaIntervalReturned
[ OK ] Search.SingleChar_CorrectSaIntervalReturned (58 ms)
[ RUN ] Search.TwoConsecutiveChars_CorrectFinalSaIntervalReturned
[ OK ] Search.TwoConsecutiveChars_CorrectFinalSaIntervalReturned (57 ms)
[ RUN ] Search.SingleCharFreqOneInText_SingleSA
[ OK ] Search.SingleCharFreqOneInText_SingleSA (57 ms)
[ RUN ] Search.TwoConsecutiveChars_SingleSaIntervalEntry
[ OK ] Search.TwoConsecutiveChars_SingleSaIntervalEntry (57 ms)
[ RUN ] Search.TwoConsecutiveCharsNoValidSaInterval_NoSearchStatesReturned
[ OK ] Search.TwoConsecutiveCharsNoValidSaInterval_NoSearchStatesReturned (57 ms)
[ RUN ] Search.SingleCharAllele_CorrectSkipToSiteStartBoundaryMarker
[ OK ] Search.SingleCharAllele_CorrectSkipToSiteStartBoundaryMarker (57 ms)
[ RUN ] Search.SingleCharAllele_SiteStartBoundarySingleSearchState
[ OK ] Search.SingleCharAllele_SiteStartBoundarySingleSearchState (56 ms)
[ RUN ] Search.FirstAlleleSingleChar_CorrectSkipToSiteStartBoundaryMarker
[ OK ] Search.FirstAlleleSingleChar_CorrectSkipToSiteStartBoundaryMarker (58 ms)
[ RUN ] Search.CharAfterSiteEndAndAllele_FourDifferentSearchStates
[ OK ] Search.CharAfterSiteEndAndAllele_FourDifferentSearchStates (56 ms)
[ RUN ] Search.GivenBoundaryMarkerAndThreeAlleles_GetAlleleMarkerSaInterval
[ OK ] Search.GivenBoundaryMarkerAndThreeAlleles_GetAlleleMarkerSaInterval (58 ms)
[ RUN ] Search.GivenBoundaryMarkerAndTwoAlleles_GetAlleleMarkerSaInterval
[ OK ] Search.GivenBoundaryMarkerAndTwoAlleles_GetAlleleMarkerSaInterval (67 ms)
[ RUN ] Search.CharAfterBoundaryEndMarker_ReturnedCorrectMarkerChars
[ OK ] Search.CharAfterBoundaryEndMarker_ReturnedCorrectMarkerChars (57 ms)
[ RUN ] Search.CharAfterBoundaryEndMarker_ReturnedCorrectSaIndexes
[ OK ] Search.CharAfterBoundaryEndMarker_ReturnedCorrectSaIndexes (57 ms)
[ RUN ] Search.CharAfterBoundaryEndMarker_ReturnedSingleCharSaIntervals
[ OK ] Search.CharAfterBoundaryEndMarker_ReturnedSingleCharSaIntervals (57 ms)
[ RUN ] Search.CharAfterBoundaryEndMarker_ReturnedSearchStatesHaveCorrectLastVariantSiteAttributes
[ OK ] Search.CharAfterBoundaryEndMarker_ReturnedSearchStatesHaveCorrectLastVariantSiteAttributes (57 ms)
[ RUN ] Search.CharAfterBoundaryEndMarker_ReturnedSearchStatesHaveCorrectVariantSiteRecordedAttributes
[ OK ] Search.CharAfterBoundaryEndMarker_ReturnedSearchStatesHaveCorrectVariantSiteRecordedAttributes (57 ms)
[ RUN ] Search.GivenAlleleMarkerSaIndex_ReturnAlleleId
[ OK ] Search.GivenAlleleMarkerSaIndex_ReturnAlleleId (56 ms)
[ RUN ] Search.ThirdAlleleSingleChar_SkipToSiteStartBoundaryMarker
[ OK ] Search.ThirdAlleleSingleChar_SkipToSiteStartBoundaryMarker (57 ms)
[ RUN ] Search.SecondAlleleSingleChar_SkipToSiteStartBoundaryMarker
[ OK ] Search.SecondAlleleSingleChar_SkipToSiteStartBoundaryMarker (57 ms)
[ RUN ] Search.FirstAlleleSingleChar_SkipToSiteStartBoundaryMarker
[ OK ] Search.FirstAlleleSingleChar_SkipToSiteStartBoundaryMarker (57 ms)
[ RUN ] Search.GivenSearchStateExitingSiteAndNextChar_CachedVariantSiteRecordedInPathHistory
[ OK ] Search.GivenSearchStateExitingSiteAndNextChar_CachedVariantSiteRecordedInPathHistory (56 ms)
[ RUN ] Search.InitialStateWithPopulatedVariantSitePath_CorrectVariantSitePathInResult
[ OK ] Search.InitialStateWithPopulatedVariantSitePath_CorrectVariantSitePathInResult (57 ms)
[ RUN ] Search.KmerAbsentFromKmerIndex_NoSearchStatesReturned
Total number of unique kmers: 1
[ OK ] Search.KmerAbsentFromKmerIndex_NoSearchStatesReturned (58 ms)
[ RUN ] Search.GivenRead_CorrectResultSaInterval
Total number of unique kmers: 1
[ OK ] Search.GivenRead_CorrectResultSaInterval (56 ms)
[ RUN ] Search.GivenReadStartingInAllele_CorrectVariantSitePath
Total number of unique kmers: 1
[ OK ] Search.GivenReadStartingInAllele_CorrectVariantSitePath (58 ms)
[ RUN ] Search.GivenReadEndingInAllele_CorrectVariantSitePath
Total number of unique kmers: 1
[ OK ] Search.GivenReadEndingInAllele_CorrectVariantSitePath (56 ms)
[ RUN ] Search.GivenReadCrossingAllele_CorrectVariantSitePath
Total number of unique kmers: 1
[ OK ] Search.GivenReadCrossingAllele_CorrectVariantSitePath (57 ms)
[ RUN ] Search.GivenReadCrossingTwoAlleles_CorrectVariantSitePath
Total number of unique kmers: 1
[ OK ] Search.GivenReadCrossingTwoAlleles_CorrectVariantSitePath (56 ms)
[ RUN ] Search.KmerWithinAlleleNotCrossingMarker_ReadCoversCorrectPath
Total number of unique kmers: 1
[ OK ] Search.KmerWithinAlleleNotCrossingMarker_ReadCoversCorrectPath (56 ms)
[ RUN ] Search.KmerImmediatelyAfterVariantSite_ReadCoversCorrectPath
Total number of unique kmers: 1
[ OK ] Search.KmerImmediatelyAfterVariantSite_ReadCoversCorrectPath (57 ms)
[ RUN ] Search.KmerCrossesVariantSite_ReadCoversCorrectPath
Total number of unique kmers: 1
[ OK ] Search.KmerCrossesVariantSite_ReadCoversCorrectPath (57 ms)
[ RUN ] Search.KmerEndsWithinAllele_ReadCoversCorrectPath
Total number of unique kmers: 1
[ OK ] Search.KmerEndsWithinAllele_ReadCoversCorrectPath (57 ms)
[ RUN ] Search.KmerCrossesMultipleVariantSites_ReadCoversCorrectPath
Total number of unique kmers: 1
[ OK ] Search.KmerCrossesMultipleVariantSites_ReadCoversCorrectPath (57 ms)
[ RUN ] Search.NoMarkersToLeft_SkippingToMarkerTrue
Total number of unique kmers: 1
[ OK ] Search.NoMarkersToLeft_SkippingToMarkerTrue (57 ms)
[ RUN ] Search.NoMarkersToLeft_DistanceToNextMarkerGreaterThanOne
Total number of unique kmers: 1
[ OK ] Search.NoMarkersToLeft_DistanceToNextMarkerGreaterThanOne (57 ms)
[ RUN ] Search.MarkerToLeft_DistanceToNextMarkerIsKmerStartTextIndex
Total number of unique kmers: 1
[ OK ] Search.MarkerToLeft_DistanceToNextMarkerIsKmerStartTextIndex (57 ms)
[ RUN ] Search.MarkerToImmediateLeft_SkippingToMarkerFlagFalse
Total number of unique kmers: 1
[ OK ] Search.MarkerToImmediateLeft_SkippingToMarkerFlagFalse (57 ms)
[ RUN ] Search.ReadLeadsToPrgEdge_NoSearchStatesFound
Total number of unique kmers: 1
[ OK ] Search.ReadLeadsToPrgEdge_NoSearchStatesFound (57 ms)
[----------] 38 tests from Search (2175 ms total)
[----------] 2 tests from BaseNextSaInterval
[ RUN ] BaseNextSaInterval.GivenC_ProcessNextCharG_CorrectSaInterval
[ OK ] BaseNextSaInterval.GivenC_ProcessNextCharG_CorrectSaInterval (57 ms)
[ RUN ] BaseNextSaInterval.GivenG_ProcessNextCharA_CorrectSaInterval
[ OK ] BaseNextSaInterval.GivenG_ProcessNextCharA_CorrectSaInterval (57 ms)
[----------] 2 tests from BaseNextSaInterval (114 ms total)
[----------] 2 tests from MarkerSearch
[ RUN ] MarkerSearch.GivenCharA_ReturnTwoCorrectSearchResults
[ OK ] MarkerSearch.GivenCharA_ReturnTwoCorrectSearchResults (56 ms)
[ RUN ] MarkerSearch.GivenCharG_ReturnOneCorrectSearchResults
[ OK ] MarkerSearch.GivenCharG_ReturnOneCorrectSearchResults (58 ms)
[----------] 2 tests from MarkerSearch (114 ms total)
[----------] Global test environment tear-down
[==========] 216 tests from 36 test cases ran. (10578 ms total)
[ PASSED ] 216 tests.
running build
running build_py
creating build
creating build/lib
creating build/lib/gramtools
copying gramtools/prg.py -> build/lib/gramtools
copying gramtools/simulate.py -> build/lib/gramtools
copying gramtools/quasimap.py -> build/lib/gramtools
copying gramtools/common.py -> build/lib/gramtools
copying gramtools/paths.py -> build/lib/gramtools
copying gramtools/build.py -> build/lib/gramtools
copying gramtools/gramtools.py -> build/lib/gramtools
copying gramtools/genome_regions.py -> build/lib/gramtools
copying gramtools/__init__.py -> build/lib/gramtools
creating build/lib/gramtools/tests
copying gramtools/tests/test_prg.py -> build/lib/gramtools/tests
copying gramtools/tests/common.py -> build/lib/gramtools/tests
copying gramtools/tests/test_genome_regions.py -> build/lib/gramtools/tests
copying gramtools/tests/test_vcf_to_linear_prg_perl.py -> build/lib/gramtools/tests
copying gramtools/tests/__init__.py -> build/lib/gramtools/tests
copying gramtools/tests/test_simulate.py -> build/lib/gramtools/tests
creating build/lib/gramtools/utils
copying gramtools/utils/__init__.py -> build/lib/gramtools/utils
creating build/lib/gramtools/version
copying gramtools/version/fallback_version.py -> build/lib/gramtools/version
copying gramtools/version/report.py -> build/lib/gramtools/version
copying gramtools/version/__init__.py -> build/lib/gramtools/version
copying gramtools/version/version.py -> build/lib/gramtools/version
running egg_info
creating gramtools.egg-info
writing dependency_links to gramtools.egg-info/dependency_links.txt
writing gramtools.egg-info/PKG-INFO
writing top-level names to gramtools.egg-info/top_level.txt
writing requirements to gramtools.egg-info/requires.txt
writing entry points to gramtools.egg-info/entry_points.txt
writing manifest file 'gramtools.egg-info/SOURCES.txt'
reading manifest file 'gramtools.egg-info/SOURCES.txt'
writing manifest file 'gramtools.egg-info/SOURCES.txt'
creating build/lib/gramtools/bin
copying gramtools/bin/gram -> build/lib/gramtools/bin
creating build/lib/gramtools/lib
copying gramtools/lib/libgramtools.a -> build/lib/gramtools/lib
copying gramtools/utils/vcf_to_linear_prg.pl -> build/lib/gramtools/utils
running install_lib
creating /apps/well/python/3.5.2-gcc5.4.0/lib/python3.5/site-packages/gramtools
error: could not create '/apps/well/python/3.5.2-gcc5.4.0/lib/python3.5/site-packages/gramtools': Permission deniedBit confused - what does pip install do - where is my gramtools?
iqbal-lab
commented
6 years ago Hm
pip3 install --user git+https://github.com/iqbal-lab-org/gramtools Collecting git+https://github.com/iqbal-lab-org/gramtools Cloning https://github.com/iqbal-lab-org/gramtools to /localhome/tmp/pip-agvawmm7-build Requirement already satisfied: Biopython in /gpfs0/apps/well/python/3.5.2-gcc5.4.0/lib/python3.5/site-packages (from gramtools==2.0) Installing collected packages: gramtools Running setup.py install for gramtools ... \lsdone Successfully installed gramtools-2.0
This looks like it has worked
-bash-4.1$ gramtools --version -bash: gramtools: command not found
ffranr
commented
6 years ago This should now be solved following commit be2838bf32ab2ee7069d45b9a3128ad8b92045c6. Will leave issue open until confirmed.
iqbal-lab
commented
6 years ago Still fails. python3 -m venv gramtools_virtualenv && source ./gramtools_virtualenv/bin/activate && pip3 install git+https://github.com/iqbal-lab-org/gramtools ... [----------] Global test environment tear-down [==========] 229 tests from 37 test cases ran. (10128 ms total) [ PASSED ] 227 tests. [ FAILED ] 2 tests, listed below: [ FAILED ] GroupedAlleleCount.GivenHashedAlleleIdsGroups_CorrectAlleleGroupsJsonString [ FAILED ] GroupedAlleleCount.GivenMultipleSites_CorrectFullJsonString
2 FAILED TESTS
ERROR: libgramtools test runner returned: 1
----------------------------------------Command "/Net/fs1/home/zam/dev/git/gramtools_virtualenv/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-axjvpqkj-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-_le0xmq9-record/install-record.txt --single-version-externally-managed --compile --install-headers /Net/fs1/home/zam/dev/git/gramtools_virtualenv/include/site/python3.5/gramtools" failed with error code 255 in /tmp/pip-axjvpqkj-build/ You are using pip version 8.1.1, however version 9.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. (gramtools_virtualenv) -bash-4.1$ gramtools --version -bash: gramtools: command not found
ffranr
commented
6 years ago Those tests don't matter, but they break the install process on some machines. I've disabled them in the latest commit. Will fix them later.
iqbal-lab
commented
6 years ago oh, ok should I try again?
ffranr
commented
6 years ago Zam reports that it works. Will open new issues if necessary.
Install fails at the end. Here's what I did
pip3 install git+https://github.com/iqbal-lab-org/gramtools
Command "/apps/well/python/3.5.2-gcc5.4.0/bin/python -u -c "import setuptools, tokenize;file='/localhome/tmp/pip-md8zizah-build/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-ojc6il3t-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /localhome/tmp/pip-md8zizah-build/
Is this the key line?
configure.ac:26: error: possibly undefined macro: m4_esyscmd_s If this token and others are legitimate, please use m4_pattern_allow.
and is it legit?
Z