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alekseyzimin / masurca

GNU General Public License v3.0
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make check fail ! #209

Open wwx734925 opened 3 years ago

wwx734925 commented 3 years ago

After the masurca was installed. runing the command: cd global-1/ && make check Is it a software problem or a configuration error?

CentOS Linux 8.2 gcc version 8.3.1

[root@cori-knl spack-src]# cd global-1/
[root@cori-knl global-1]# make check
Making check in jellyfish
make[1]: Entering directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
make  check-am
make[2]: Entering directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
make  libgtest.la libgtest_main.la bin/generate_sequence bin/fastq2sam bin/test_all
make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
  CXX      unit_tests/gtest/src/libgtest_la-gtest-all.lo
  CXXLD    libgtest.la
  CXX      unit_tests/gtest/src/libgtest_main_la-gtest_main.lo
  CXXLD    libgtest_main.la
  CXX      jellyfish/generate_sequence.o
  CXX      jellyfish/mersenne.o
  CXX      jellyfish/backtrace.o
  CXX      jellyfish/dbg.o
  CXXLD    bin/generate_sequence
  CXX      jellyfish/fastq2sam.o
  CXXLD    bin/fastq2sam
  CXX      unit_tests/bin_test_all-test_main.o
  CXX      unit_tests/bin_test_all-test_misc.o
  CXX      unit_tests/bin_test_all-test_offsets_key_value.o
  CXX      unit_tests/bin_test_all-test_simple_circular_buffer.o
  CXX      unit_tests/bin_test_all-test_rectangular_binary_matrix.o
  CXX      unit_tests/bin_test_all-test_mer_dna.o
  CXX      unit_tests/bin_test_all-test_large_hash_array.o
  CXX      unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o
  CXX      unit_tests/bin_test_all-test_file_header.o
  CXX      unit_tests/bin_test_all-test_mer_iterator.o
  CXX      unit_tests/bin_test_all-test_hash_counter.o
  CXX      unit_tests/bin_test_all-test_mer_heap.o
  CXX      unit_tests/bin_test_all-test_stream_iterator.o
  CXX      unit_tests/bin_test_all-test_token_ring.o
  CXX      unit_tests/bin_test_all-test_text_dumper.o
  CXX      unit_tests/bin_test_all-test_dumpers.o
  CXX      unit_tests/bin_test_all-test_mapped_file.o
  CXX      unit_tests/bin_test_all-test_int128.o
  CXX      unit_tests/bin_test_all-test_mer_dna_bloom_counter.o
  CXX      unit_tests/bin_test_all-test_whole_sequence_parser.o
  CXX      unit_tests/bin_test_all-test_allocators_mmap.o
  CXX      unit_tests/bin_test_all-test_cooperative_pool2.o
  CXX      unit_tests/bin_test_all-test_generator_manager.o
  CXX      unit_tests/bin_test_all-test_atomic_bits_array.o
  CXX      unit_tests/bin_test_all-test_stdio_filebuf.o
  CXX      jellyfish/bin_test_all-backtrace.o
  CXXLD    bin/test_all
make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
make  check-TESTS
make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
FAIL: tests/generate_sequence.sh
FAIL: tests/parallel_hashing.sh
FAIL: tests/merge.sh
FAIL: tests/bloom_filter.sh
FAIL: tests/big.sh
FAIL: tests/subset_hashing.sh
FAIL: tests/multi_file.sh
FAIL: tests/bloom_counter.sh
FAIL: tests/large_key.sh
FAIL: tests/sam.sh
FAIL: tests/swig_python.sh
FAIL: tests/swig_ruby.sh
FAIL: tests/swig_perl.sh
FAIL: unit_tests/unit_tests.sh
============================================================================
Testsuite summary for global 1
============================================================================
# TOTAL: 14
# PASS:  0
# SKIP:  0
# XFAIL: 0
# FAIL:  14
# XPASS: 0
# ERROR: 0
============================================================================
See jellyfish/test-suite.log
Please report to gmarcais@umd.edu
============================================================================
make[4]: *** [Makefile:2214: test-suite.log] Error 1
make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
make[3]: *** [Makefile:2322: check-TESTS] Error 2
make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
make[2]: *** [Makefile:2386: check-am] Error 2
make[2]: Leaving directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
make[1]: *** [Makefile:2388: check] Error 2
make[1]: Leaving directory '/tmp/root/spack-stage/spack-stage-masurca-3.3.1-cmwrevecosg66wxbws4u2fuowsqeljbi/spack-src/global-1/jellyfish'
make: *** [Makefile:432: check-recursive] Error 1
[root@cori-knl global-1]#
alekseyzimin commented 3 years ago

To install masurca, please download the tarball from the "releases", untar/unzip and then run ./configure make make install as described in the README. make check is not guaranteed to work on release tarball.

alekseyzimin commented 3 years ago

Please also make sure you use the latest version 3.4.3