Check fclose(stdout) at the end of main() [and miscellanea] #2046
Cirrus CI / ubuntu-clang CFLAGS:-g -Wall -O3 -fsanitize=address LDFLAGS:-fsanitize=address -Wl,-rpath,`pwd`/inst/lib USE_CONFIG:yes
failed
Jan 9, 2024 in 3m 11s
Task Summary
Instruction test failed in 01:19
Details
✅ 00:02 clone
✅ 00:19 install
✅ 00:01 htslib_clone
✅ 01:26 compile
❌ 01:19 test
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -h /tmp/cirrus-ci-build/test/reheader.empty.hdr /tmp/6OMPawfKdP/empty.vcf.gz | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
cat /tmp/6OMPawfKdP/empty.vcf.gz | /tmp/cirrus-ci-build/bcftools reheader -h /tmp/cirrus-ci-build/test/reheader.empty.hdr | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -f /tmp/cirrus-ci-build/test/reheader.fai /tmp/cirrus-ci-build/test/reheader.2.vcf | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -f /tmp/cirrus-ci-build/test/reheader.fai /tmp/6OMPawfKdP/reheader.2.bcf | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -f /tmp/cirrus-ci-build/test/reheader.fai /tmp/6OMPawfKdP/reheader.2.vcf.gz | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -h /tmp/cirrus-ci-build/test/reheader.2.hdr -f /tmp/cirrus-ci-build/test/reheader.fai /tmp/cirrus-ci-build/test/reheader.2.vcf | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -h /tmp/cirrus-ci-build/test/reheader.2.hdr -f /tmp/cirrus-ci-build/test/reheader.fai /tmp/6OMPawfKdP/reheader.2.bcf | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -h /tmp/cirrus-ci-build/test/reheader.2.hdr -f /tmp/cirrus-ci-build/test/reheader.fai /tmp/6OMPawfKdP/reheader.2.vcf.gz | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -f /tmp/cirrus-ci-build/test/reheader.3.fai /tmp/cirrus-ci-build/test/reheader.3.vcf | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -f /tmp/cirrus-ci-build/test/reheader.3.fai /tmp/6OMPawfKdP/reheader.3.bcf | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
test_vcf_reheader:
/tmp/cirrus-ci-build/bcftools reheader -f /tmp/cirrus-ci-build/test/reheader.3.fai /tmp/6OMPawfKdP/reheader.3.vcf.gz | /tmp/cirrus-ci-build/bcftools view --no-version
.. ok
[E::main] closing standard output failed
The command failed: /tmp/cirrus-ci-build/bcftools query -f'chr%CHROM\t%POS\n' /tmp/cirrus-ci-build/test/annotate.vcf > /tmp/cirrus-ci-build/test/rename.out.tmp
at ./test/test.pl line 943.
main::error("The command failed: /tmp/cirrus-ci-build/bcftools query -f'ch"..., "") called at ./test/test.pl line 1089
main::cmd("/tmp/cirrus-ci-build/bcftools query -f'chr%CHROM\\t%POS\\n' /tm"...) called at ./test/test.pl line 1815
main::test_rename_chrs(HASH(0x5b9df9dd44b8), "in", "annotate") called at ./test/test.pl line 1031
main::run_test(CODE(0x5b9dfa5844c0), HASH(0x5b9df9dd44b8), "in", "annotate") called at ./test/test.pl line 761
make: *** [Makefile:314: test-plugins] Error 1
Exit status: 2
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