Tests 10-12 fail
hepcat72 opened this issue · 2 comments
hepcat72 commented
I don't know if this is specific to my system (macOS Catalina 10.15.6), but tests 10-12 fail due to a segfault (on master):
sh: line 1: 98519 Segmentation fault: 11 ../fastq-multx -H -v ' ' -l in/multx/master-barcodes.txt in/multx/mxtest-h_1.fastq in/multx/mxtest-h_2.fastq -o tmp/multx.t.R0jAb/mxout_%_1.fq -o tmp/multx.t.R0jAb/mxout_%_2.fq > tmp/multx.t.R0jAb/test4.out 2> tmp/multx.t.R0jAb/test4.err
not ok 10 - test4 worked (../fastq-multx -H -v ' ' -l in/multx/master-barcodes.txt in/multx/mxtest-h_1.fastq in/multx/mxtest-h_2.fastq -o tmp/multx.t.R0jAb/mxout_%_1.fq -o tmp/multx.t.R0jAb/mxout_%_2.fq > tmp/multx.t.R0jAb/test4.out 2> tmp/multx.t.R0jAb/test4.err)
# Failed test 'test4 worked (../fastq-multx -H -v ' ' -l in/multx/master-barcodes.txt in/multx/mxtest-h_1.fastq in/multx/mxtest-h_2.fastq -o tmp/multx.t.R0jAb/mxout_%_1.fq -o tmp/multx.t.R0jAb/mxout_%_2.fq > tmp/multx.t.R0jAb/test4.out 2> tmp/multx.t.R0jAb/test4.err)'
# at multx.t line 25.
not ok 11 - Files equal: tmp/multx.t.R0jAb/test4.out == out/multx/test4.out
# Failed test 'Files equal: tmp/multx.t.R0jAb/test4.out == out/multx/test4.out'
# at ./test-prep.pl line 48.
not ok 12 - Files equal: tmp/multx.t.R0jAb/test4.err == out/multx/test4.err
# Failed test 'Files equal: tmp/multx.t.R0jAb/test4.err == out/multx/test4.err'
# at ./test-prep.pl line 48.
hepcat72 commented
Hmmm, after the latest merge, this doesn't seem to be an issue, however with this version, test 8 fails because the standard output rows are in a different order. Weird. I assume there's some sort of hash scheme or something where the traversal of elements can change...
hepcat72 commented
After looking into this, I believe that the segfaults are from compiling without doing a make clean
first. The segfaults for these tests go away if I recompile after doing a make clean.