source: python-biopython version: 1.79+dfsg-1 severity: serious tags: patch
muscle was recently removed from most architectures[1], leaving python-biopython's build-dependencies unsatisfiable on those architectures. The build-dependency is already marked as nocheck so presumably is only used for tests. I added an architecture restriction to the dependency and was able to perform a successfully test build in an environment without muscle installed. Note that I used python3-fonttools from testing for the test build as unstable's version is currently uninstallable. A debdiff is attached. The recent upload of python-biopython 1.79+dfsg-2 also moved w3-dtd-mathml from Suggests to Depends. Unfortunately w3-dtd-mathml is rc buggy[2] and not in testing. There is a patch available for the rc bug, but discussion in the bug report suggests that it may be better to migrate to w3c-sgml-lib which has a newer version of the mathml dtd. [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006161 [2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=994795
diff -Nru python-biopython-1.79+dfsg/debian/changelog python-biopython-1.79+dfsg/debian/changelog --- python-biopython-1.79+dfsg/debian/changelog 2022-02-17 19:15:09.000000000 +0000 +++ python-biopython-1.79+dfsg/debian/changelog 2022-03-01 20:39:50.000000000 +0000 @@ -1,3 +1,11 @@ +python-biopython (1.79+dfsg-2.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Restrict architecture list of muscle build-dependency to reflect + architectures where the current version of muscle is available. + + -- Peter Michael Green <plugw...@debian.org> Tue, 01 Mar 2022 20:39:50 +0000 + python-biopython (1.79+dfsg-2) unstable; urgency=medium * Move w3-dtd-mathml from Suggests to Depends to avoid dangling symlink diff -Nru python-biopython-1.79+dfsg/debian/control python-biopython-1.79+dfsg/debian/control --- python-biopython-1.79+dfsg/debian/control 2022-02-17 19:15:09.000000000 +0000 +++ python-biopython-1.79+dfsg/debian/control 2022-03-01 20:39:50.000000000 +0000 @@ -25,7 +25,7 @@ emboss <!nocheck>, fasttree <!nocheck>, mafft <!nocheck>, - muscle <!nocheck>, + muscle [i386 amd64 x32] <!nocheck>, ncbi-blast+ <!nocheck>, phylip <!nocheck>, phyml [any-amd64 any-i386] <!nocheck>,