Source: ariba Version: 2.14.6+ds-3 Severity: serious Tags: ftbfs upstream help Justification: fails to build from source (but built successfully in the past)
Greetings, Following the upgrade of htslib, samtools and bcftools from versions 1.13 to 1.16, ariba hits autopkgtest regressions which are preventing migration of python-pysam to testing. The test failures are also present during the build time test suite, causing the package to fail to build from source. I attempted to begin wrapping up a patch fixing/working around the problem which looks to be caused by the migration of mpileup functionalities from samtools to bcftools, but the test suite then chokes on non-matching command output, for which I don't know whether the new results are sound and simply need adjustments, or if errors could have been left over. Temporary patch is below for reference, but is not sufficient on his own to fix the failure: -------8<--------------8<--------------8<--------------8<------- --- a/ariba/samtools_variants.py +++ b/ariba/samtools_variants.py @@ -1,6 +1,7 @@ import os import sys import pysam +import pysam.bcftools import pyfastaq import vcfcall_ariba @@ -36,13 +37,11 @@ tmp_vcf = self.vcf_file + '.tmp' with open(tmp_vcf, 'w') as f: - print(pysam.mpileup( + print(pysam.bcftools.mpileup( '-t', 'INFO/AD,INFO/ADF,INFO/ADR', '-L', '99999999', '-A', '-f', self.ref_fa, - '-u', - '-v', self.bam, ), end='', file=f) -------8<--------------8<--------------8<--------------8<------- I already provided upstream with my findings on their issue tracker[1] in a related entry, but I don't know for sure how much active they are these days. This note in debbugs is mostly to document the issue for Med team members before they spend too much time debugging this issue in parallel (and also seeking help if possible). [1]: https://github.com/sanger-pathogens/ariba/issues/327 Have a nice day, :) Étienne. -- System Information: Debian Release: bookworm/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.19.0-2-amd64 (SMP w/12 CPU threads; PREEMPT) Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled -- Étienne Mollier <emoll...@emlwks999.eu> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/5, please excuse my verbosity. On air: Gazpacho - Valerie's Friend
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