Hello Andreas, On Mon, Nov 26, 2018 at 08:08:44AM +0100, Andreas Tille wrote: > version 1.14.11 of staden-io-lib creates an error in the test suite for non > x86 > architectures. Here you have an easy overview what architectures are > affected: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__buildd.debian.org_status_package.php-3Fp-3Dstaden-2Dio-2Dlib-26suite-3Dsid&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=wodoR_G062E4YLZ-xu5t6g&m=L-jZYyQAt7E4nbUsttBpOY_Mp4v3CCgPpbF36FyJveI&s=-atiCd8AX9Plf89RpXOx6vaJ9hAbqKhJ27ntOhiECy4&e=
Sorry for the butchered URL. I hate our new email scanning! I looked at this and don't see test failures, only "build attempted". Has it changed since this email? > and this is basically the failure. Do you have any idea how to fix this? > > ... > FAIL: scram > =========== > > Loading ce.fa > Generating ce#sorted.sam > Generating ce#unsorted.sam > === testing ./data/c1#bounds.sam === > ./scram.test: 27: [: ./data/c1#bounds.sam: unexpected operator > ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.sam > ../progs/scramble -r ./data/c1.fa ./data/c1#bounds.sam > test.out/c1#bounds.full.cram > ../progs/scramble ./data/c1#bounds.sam > test.out/tmp.sam > ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam > ../progs/scramble -O bam test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.bam > ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam > corrupted size vs. prev_size > Aborted > FAIL scram.test (exit status: 1) I'm also struggling to find the "corrupted size vs. prev_size" error message anywhere in the code, not even "prev_size". Googling for it I finally found it listed as an error in GNU malloc, which possibly means there is a memory corruption. I will run through the entire test harness using address sanitiser and if that doesn't work with Valgrind. James -- James Bonfield (j...@sanger.ac.uk) The Sanger Institute, Hinxton, Cambs, CB10 1SA -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
