Hi Andreas, Le 03/02/2023 à 11:17, Andreas Tille a écrit :
Hi, I realised that snippy autopkgtest is failing for i386 and s390x[1] The log for i386[2] says: Get:310 http://deb.debian.org/debian testing/main i386 libsnpeff-java all 5.1+d+dfsg-3 [2,150 kB] ... [16:13:15] Found snpEff - /usr/bin/snpEff ... [16:13:15] Found snippy-vcf_to_tab - /usr/bin/snippy-vcf_to_tab [16:13:15] Found snippy-vcf_report - /usr/bin/snippy-vcf_report [16:13:15] Checking version: samtools --version is >= 1.7 - ok, have 1.16 [16:13:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.16 [16:13:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.6 [16:13:15] Need snpEff -version >= 4.3 but you have 0 - please upgrade it. autopkgtest [16:13:16]: test run-unit-test: -----------------------] I have no idea what this might mean.
In fact it turns out snpeff itself is not installable on i386. I just tried to apt-get install snpeff in an i386 chroot and I got
-------------------------------8<------------------------------------ Reading package lists... Building dependency tree... Reading state information... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies:libngs-java : Depends: libngs-jni (>= 3.0.3+dfsg-4) but it is not installable Depends: libngs-jni (< 3.0.3+dfsg-4.1~) but it is not installable
E: Unable to correct problems, you have held broken packages. Command apt-get --dry-run install -- snpeff exited with exit code 1. -------------------------------8<------------------------------------libngs-jni and libngs-java are built from src:sra-sdk, of which binaries are only for amd64 and arm64, see [3]. Thus we could ignore autopkgtest failures on arches other than amd64 and arm64 for snippy -- although I cannot explain right now how its autopkgtests are passing on armel for instance, as libngs-jni is unavailable there.
Meanwhile I've pushed a change to ignore s390x architecture for debci since
the required bcftools does not exist here.
Kind regards
Andreas.
[1] https://qa.debian.org/excuses.php?package=snippy
[2] https://ci.debian.net/data/autopkgtest/testing/i386/s/snippy/30738457/log.gz
Would you have time today, you can take a decision if it is obvious to you. Else I will look at it during the weekend!
Best, -- Pierre [3] https://buildd.debian.org/status/package.php?p=sra-sdk
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