[med-svn] [Git][med-team/bioperl-run][master] 2 commits: do not run tests parallel to get sensibly sorted output

[Andreas Tille]

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 <tille at debian.org>  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
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