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atifrahman / HAWK

Hitting associations with k-mers
GNU General Public License v3.0
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make check tests failed; #24

Open robertwhbaldwin opened 3 years ago

robertwhbaldwin commented 3 years ago

I was wondering about the following test failures/skips. The modified version of Jellyfish2 installed correctly without error but when I ran make check some tests were skipped/failed which should not have from what I understand. Opening up those scripts it seems to me these might be computer resource issues (not enough memory) so I'll try on a better machine. If anyone can suggest what the problem might be I'd appreciate it. - Robert

ake[3]: Entering directory '/home/ubuntu/HAWK/supplements/jellyfish-2.2.10' PASS: tests/generate_sequence.sh FAIL: tests/parallel_hashing.sh PASS: tests/merge.sh PASS: tests/bloom_filter.sh SKIP: tests/big.sh PASS: tests/subset_hashing.sh PASS: tests/multi_file.sh PASS: tests/bloom_counter.sh FAIL: tests/large_key.sh SKIP: tests/sam.sh PASS: tests/small_mers.sh SKIP: tests/swig_python.sh SKIP: tests/swig_ruby.sh SKIP: tests/swig_perl.sh PASS: unit_tests/unit_tests.sh make[4]: Entering directory '/home/ubuntu/HAWK/

robertwhbaldwin commented 3 years ago

This was not a resource issue. I get the same output if I try to make check on the unmodified jellyfish version 2.10. On the other hand I'm able to run the countKmer script and get a properly formatted kmer count output file, see below. So I don't know if there's a problem with unmet dependencies for jellyfish. And I don't know if the failed tests have caused problems with the output. But the output looks fine and there's no error messages coming from the countKmer script. Does anyone think that the failed tests are important for kmer counting? - RObert

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robertwhbaldwin commented 3 years ago

While reading through the Issues for jellyfish I found out that these tests can fail for trivial reasons and jellyfish will run correctly But the doc states that they should pass which is confusing. So it was nothing to worry about.