Andreas Tille pushed to branch master at Debian Med / bioperl-run
Commits: c2700f24 by Andreas Tille at 2018-09-14T12:11:12Z do not run tests parallel to get sensibly sorted output - - - - - 407c1747 by Andreas Tille at 2018-09-14T12:46:28Z Allow MPI oversubscription (as in phyml build since phyml caused problems inside build time tests) - - - - - 3 changed files: - debian/changelog - debian/control - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +bioperl-run (1.7.2-4) UNRELEASED; urgency=medium + + * (Build-)Depends: ncoils + * do not run tests parallel to get sensibly sorted output + * Allow MPI oversubscription (as in phyml build since phyml caused + problems inside build time tests) + Closes: #906337 + + -- Andreas Tille <[email protected]> Fri, 14 Sep 2018 13:22:55 +0200 + bioperl-run (1.7.2-3) unstable; urgency=medium * Drop adjust_bowtie_tests.patch, Closes: #887578 ===================================== debian/control ===================================== @@ -35,6 +35,7 @@ Build-Depends-Indep: perl, maq, mafft, muscle, + ncoils, phylip, phyml, primer3, @@ -73,6 +74,7 @@ Recommends: amap-align, maq, mafft, muscle, + ncoils, phylip, phyml, primer3, @@ -92,7 +94,6 @@ Suggests: gmap, # The following list of packages is not available in Debian: # blat, # cap3, -# coils, # condense, # drawgram, # drawtree, @@ -136,7 +137,7 @@ Suggests: gmap, # tigr-assembler, # tmhmm, # tribe, -# trnascan, +# trnascan-se, # non-free # vista-align Description: BioPerl wrappers: scripts Contains scripts from the BioPerl-Run package. This package will also install ===================================== debian/rules ===================================== @@ -21,6 +21,7 @@ FAILING_TESTS_FOR_DUE_TO_MISSING_MODULES=BWA \ # Important for hyphympi # See https://lists.debian.org/debian-science/2012/03/msg00005.html export OMPI_MCA_plm_rsh_agent=/bin/false +export OMPI_MCA_rmaps_base_oversubscribe=1 %: dh $@ @@ -29,10 +30,12 @@ override_dh_auto_configure: dh_auto_configure -- --install_scripts $(NETWORK) override_dh_auto_test: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) mkdir t.skip for t in $(NOT_SUPPORTED_TESTS) $(FAILING_TESTS_FOR_DUE_TO_MISSING_MODULES) ; do mv t/$${t}.t t.skip ; done PATH=$$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin \ HOME_4_TCOFFEE=/tmp \ - dh_auto_test + dh_auto_test --no-parallel mv t.skip/* t rm -rf t.skip +endif View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/compare/c559c463e55181ab8c31814dc9aa160dae439013...407c1747df94cc8c46493f40a6d5ab792b936635 -- View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/compare/c559c463e55181ab8c31814dc9aa160dae439013...407c1747df94cc8c46493f40a6d5ab792b936635 You're receiving this email because of your account on salsa.debian.org.
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