Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits: 8ea33aeb by Étienne Mollier at 2020-09-20T18:55:06+02:00 Sides of #969608 have been addressed The work around is removed in favor of using the ncbi-blast+ 2.10.1-1 or later. - - - - - 13965712 by Étienne Mollier at 2020-09-20T19:31:36+02:00 updated d/changelog accordingly - - - - - 3e9ded59 by Étienne Mollier at 2020-09-20T19:47:48+02:00 add python3-biopython.lintian-overrides - - - - - 44b72355 by Étienne Mollier at 2020-09-23T20:39:32+02:00 d/control: build-dep on ncbi-blast+ >= 2.10.1-2 This version addresses FTBFS on mipsel. - - - - - 8db76075 by Étienne Mollier at 2020-10-02T23:16:54+02:00 d/changelog a bit more comprehensive, hopefully - - - - - 63ba5cc1 by Étienne Mollier at 2020-10-02T23:23:49+02:00 routine-update: Ready to upload to unstable - - - - - 4 changed files: - debian/changelog - debian/control - + debian/python3-biopython.lintian-overrides - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,10 +1,13 @@ -python-biopython (1.78+dfsg-2) UNRELEASED; urgency=medium +python-biopython (1.78+dfsg-2) unstable; urgency=medium - * Added DEP3 description to blastdbv4-tests-filter-archs.patch. - * Removed, at last, patch working around makeblastd bug in v5. - * Reviewed and forwarded patches upstream when applicable. + * Bumped build requirement on ncbi-blast+ 2.10.1-2 and greater: + - fixed building on mipsel; + - removed patch working around makeblastdb bug in v5, now unnecessary. + * Cleaned up patches: + - added DEP3 description to blastdbv4-tests-filter-archs.patch; + - reviewed and forwarded patches upstream when applicable. - -- Étienne Mollier <[email protected]> Mon, 14 Sep 2020 21:28:54 +0200 + -- Étienne Mollier <[email protected]> Fri, 02 Oct 2020 23:18:07 +0200 python-biopython (1.78+dfsg-1) unstable; urgency=medium ===================================== debian/control ===================================== @@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 13), fasttree <!nocheck>, mafft <!nocheck>, muscle <!nocheck>, - ncbi-blast+ (>= 2.10.0-3) <!nocheck>, + ncbi-blast+ (>= 2.10.1-2) <!nocheck>, phylip <!nocheck>, phyml [any-amd64 any-i386] <!nocheck>, prank <!nocheck>, ===================================== debian/python3-biopython.lintian-overrides ===================================== @@ -0,0 +1,3 @@ +# This link has been introduced with the resolution of #672407 and might not +# be as much a concern as if it were an architecture dependent shared object. +breakout-link usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd -> usr/share/xml/schema/w3c/mathml/dtd/mathml2.dtd ===================================== debian/rules ===================================== @@ -34,15 +34,6 @@ else EXCLUDEARCHamd64=raxml_tool endif -# arm64 virtualized environment, esp. with schroot, may be too constrained for -# the memory allocation required by the test_NCBI_BLAST_tools. See #969608 -# following for more details: -# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40 -ifeq ($(BUILDARCH),arm64) - export BLASTDB_LMDB_MAP_SIZE=20000000000 -endif - - # avoid tests requiring data base connections if no server is running while we are doing the build # This would not trigger a failure but bloats the build log with irrelevant noise EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2 View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/f4f41aebd08313023b535681e6a1a283b8f9d788...63ba5cc15fdf74f88bd71ebbfafcbcd3f49e0b50 -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/f4f41aebd08313023b535681e6a1a283b8f9d788...63ba5cc15fdf74f88bd71ebbfafcbcd3f49e0b50 You're receiving this email because of your account on salsa.debian.org.
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