Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits: 5eb9ae49 by Étienne Mollier at 2020-10-05T18:35:35+02:00 Revert "routine-update: Ready to upload to unstable" This reverts commit 632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc. - - - - - 78a0389a by Étienne Mollier at 2020-10-05T18:43:47+02:00 d/rules: erased makeblastdb override should be properly handled by all architectures now. - - - - - b1bfd6c8 by Étienne Mollier at 2020-10-05T18:44:48+02:00 d/tests/run-unit-tests: removed makeblastdb override this should be properly handled on all architectures, including mipsel, since ncbi-blast+ 2.10.1-3. Also, the override that was still present in that file could have been a source of autopkgtest failures. - - - - - 4046757b by Étienne Mollier at 2020-10-05T18:49:17+02:00 d/control: bump requirement to ncbi-blast+ 2.10.1-3 - - - - - 2b9339e1 by Étienne Mollier at 2020-10-05T19:26:14+02:00 updated d/changelog to reflect changes appropriately - - - - - 4 changed files: - debian/changelog - debian/control - debian/rules - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,10 +1,9 @@ -python-biopython (1.78+dfsg-3) unstable; urgency=medium +python-biopython (1.78+dfsg-3) UNRELEASED; urgency=medium - * mpisel build still failing on buildd (host arch mips64el, schroot mipsel) - - overred makeblastdb memory allocation for that arch on build and test; - - updated run-unit-test to reflect that change. + * Bumped ncbi-blast+ version requirement to 2.10.1-3 + * Made sure run-unit-test did not attempt memory allocation override - -- Étienne Mollier <[email protected]> Sun, 04 Oct 2020 22:18:45 +0200 + -- Étienne Mollier <[email protected]> Sat, 03 Oct 2020 10:34:12 +0200 python-biopython (1.78+dfsg-2) unstable; urgency=medium ===================================== debian/control ===================================== @@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 13), fasttree <!nocheck>, mafft <!nocheck>, muscle <!nocheck>, - ncbi-blast+ (>= 2.10.1-2) <!nocheck>, + ncbi-blast+ (>= 2.10.1-3) <!nocheck>, phylip <!nocheck>, phyml [any-amd64 any-i386] <!nocheck>, prank <!nocheck>, @@ -58,7 +58,7 @@ Depends: ${python3:Depends}, ${misc:Depends}, python3-reportlab Recommends: python-biopython-doc (= ${source:Version}), - ncbi-blast+ (>= 2.10.0-3) + ncbi-blast+ (>= 2.10.1-3) Suggests: python3-tk, bwa, clustalo, ===================================== debian/rules ===================================== @@ -34,14 +34,6 @@ else EXCLUDEARCHamd64=raxml_tool endif -# virtualized environment, esp. with schroot, may be too constrained for the -# memory allocation required by the test_NCBI_BLAST_tools. See #969608 for -# more details: -# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40 -ifeq ($(BUILD_ARCH),mipsel) - export BLASTDB_LMDB_MAP_SIZE = 3000000000 -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 ===================================== debian/tests/run-unit-test ===================================== @@ -27,15 +27,6 @@ if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" != "amd64" ]; then rm -f test_BWA_tool.py fi -# virtualized environment, esp. with schroot, may be too constrained for the -# memory allocation required by the test_NCBI_BLAST_tools. See #969608 for -# more details: -# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40 -if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "mipsel" ]; then - BLASTDB_LMDB_MAP_SIZE=3000000000 - export BLASTDB_LMDB_MAP_SIZE -fi - # execute tests ################################################################################ # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc...2b9339e183b1d4999bbeaddab1b5d92184594c98 -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc...2b9339e183b1d4999bbeaddab1b5d92184594c98 You're receiving this email because of your account on salsa.debian.org.
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