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sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file
http://sanger-pathogens.github.io/snp-sites/
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Failing tests on various platforms #51

Closed satta closed 8 years ago

satta commented 8 years ago

The test suite for 2.2.2 fails with a bunch of tests on various platforms, e.g. i386. Here's the message:

FAIL: run-all-tests
=========================================
   snp-sites 2.2.2: src/test-suite.log
=========================================

# TOTAL: 1
# PASS:  0
# SKIP:  0
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: run-all-tests
===================

Running suite(s): Creating_SNP_Sites
Alignment ../tests/data/uneven_alignment.aln contains sequences of unequal length. Expected length is 8 but got 9 in sequence Uneven_number_of_bases

76%: Checks: 21, Failures: 5, Errors: 0
../tests/check-snp-sites.c:40:F:snp_sites:valid_alignment_with_one_line_per_sequence:0: Invalid VCF file for 1 line per seq
../tests/check-snp-sites.c:79:F:snp_sites:valid_alignment_with_multiple_lines_per_sequence:0: Invalid VCF file for multiple lines per seq
../tests/check-snp-sites.c:67:F:snp_sites:valid_alignment_with_one_line_per_sequence_gzipped:0: Invalid VCF file for 1 line per seq
../tests/check-snp-sites.c:53:F:snp_sites:valid_alignment_with_n_as_gap:0: Invalid VCF file for 1 line per seq
../tests/check-snp-sites.c:132:F:snp_sites:valid_with_all_outputted_with_custom_name:0: Custom name needs extra extension for VCF
Running suite(s): Creating_VCF_file
100%: Checks: 3, Failures: 0, Errors: 0
FAIL run-all-tests (exit status: 1)

============================================================================
Testsuite summary for snp-sites 2.2.2
============================================================================
# TOTAL: 1
# PASS:  0
# SKIP:  0
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0
============================================================================
See src/test-suite.log
============================================================================

A full log is at https://buildd.debian.org/status/fetch.php?pkg=snp-sites&arch=i386&ver=2.2.2-1&stamp=1458222828 for example.

I can reproduce this on a Jessie i386 Vagrant box. A quick bisect flagged commit b2efeb4288d4201480408b7dfe3e314c243e53c6 as the first bad one, but I'm not familiar enough with what is being tested to say more.

andrewjpage commented 8 years ago

Hopefully it should be fixed in 2.3.0

satta commented 8 years ago

Nice, thanks! Waiting for the tag, then I'll update the build.

satta commented 8 years ago

Builds are fixed now, many thanks!