Hi Pierre,
Am Fri, Feb 03, 2023 at 11:32:07AM +0100 schrieb Pierre Gruet:
> > [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
Strange that this log is that different from s390x where the
installation issue is more direct, but in principle the same.
> -------------------------------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.
I think with this explanation the conclusion should be
diff --git a/debian/tests/control b/debian/tests/control
index cd113c6..fd46ed1 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -1,4 +1,4 @@
Tests: run-unit-test
Depends: @
Restrictions: allow-stderr, skip-not-installable
-Architecture: !s390x
+Architecture: amd64 arm64
which I'll upload soon.
> 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!
IMHO we need to decide whether we should ship snpeff version 5.0 rather
than 5.1 to deal with bug #1029202. May be you can estimate the effort
needed for this change? I have no idea how many applications besides
snippy are suffering from this issue but it does not sound good.
Kind regards
Andreas.
> [3] https://buildd.debian.org/status/package.php?p=sra-sdk
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