[med-svn] [Git][med-team/python-biopython][master] 6 commits: Sides of #969608 have been addressed

[Étienne Mollier]

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 <etienne.mollier at mailoo.org>  Mon, 14 Sep 2020 21:28:54 +0200
+ -- Étienne Mollier <etienne.mollier at mailoo.org>  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
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