[med-svn] r23293 - trunk/packages/bioperl-run/trunk/debian

[Andreas Tille]

Author: tille
Date: 2016-12-16 09:58:28 +0000 (Fri, 16 Dec 2016)
New Revision: 23293

Modified:
   trunk/packages/bioperl-run/trunk/debian/changelog
   trunk/packages/bioperl-run/trunk/debian/control
   trunk/packages/bioperl-run/trunk/debian/rules
Log:
Try to run unit tests which failed blatantly with bioperl 1.7.1.  Just commit this status to enable other reproducing this without any decision whether the final package should remain with the unit tests.


Modified: trunk/packages/bioperl-run/trunk/debian/changelog
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/changelog	2016-12-16 08:09:29 UTC (rev 23292)
+++ trunk/packages/bioperl-run/trunk/debian/changelog	2016-12-16 09:58:28 UTC (rev 23293)
@@ -1,3 +1,14 @@
+bioperl-run (1.6.9-4) UNRELEASED; urgency=medium
+
+  * Testsuite: autopkgtest-pkg-perl
+  * cme fix dpkg-control
+  * Enable lots of tests
+  TODO: not sure whether this should remain for the package release but
+        for the moment we need to verify functionality with latest bioperl
+  * Fix homepage
+
+ -- Andreas Tille <tille at debian.org>  Fri, 16 Dec 2016 09:17:37 +0100
+
 bioperl-run (1.6.9-3) unstable; urgency=medium
 
   [ Charles Plessy ]

Modified: trunk/packages/bioperl-run/trunk/debian/control
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/control	2016-12-16 08:09:29 UTC (rev 23292)
+++ trunk/packages/bioperl-run/trunk/debian/control	2016-12-16 09:58:28 UTC (rev 23293)
@@ -3,11 +3,12 @@
 Uploaders: Charles Plessy <plessy at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
+Testsuite: autopkgtest-pkg-perl
 Priority: optional
 Build-Depends: debhelper (>= 9)
 Build-Depends-Indep: perl,
                      libmodule-build-perl,
-                     bioperl (>= 1.6.9),
+                     bioperl,
 # Recommended in Build.PL:
                      libalgorithm-diff-perl,
                      libipc-run-perl,
@@ -15,18 +16,38 @@
                      libxml-twig-perl,
 # Not yet available: libfile-sort-perl
 # Needed for the tests, but not documented Upstream
+                     libtest-most-perl,
                      libarray-compare-perl,
                      libtree-dagnode-perl,
 # Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup.
-# amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate,
-# hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probcons,
-# samtools, sim4, t-coffee, tigr-glimmer, wise,
+                     amap-align,
+                     bedtools,
+                     blast2,
+                     bowtie,
+                     bwa,
+                     clustalw,
+                     emboss,
+                     exonerate,
+                     hmmer,
+                     infernal,
+                     kalign,
+                     maq,
+                     mafft,
+                     muscle,
+                     phyml,
+                     primer3,
+                     probcons,
+                     samtools,
+                     sim4,
+                     t-coffee,
+                     tigr-glimmer,
+                     wise,
 # Needed for the network tests:
                      libwww-perl
-Standards-Version: 3.9.6
+Standards-Version: 3.9.8
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bioperl-run/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bioperl-run/trunk/
-Homepage: http://www.bioperl.org/wiki/Run_package
+Homepage: http://search.cpan.org/dist/BioPerl-Run/
 
 Package: bioperl-run
 Architecture: all
@@ -48,6 +69,7 @@
             maq,
             mafft,
             muscle,
+            phylip,
             phyml,
             primer3,
             probalign,
@@ -57,13 +79,11 @@
             t-coffee,
             tigr-glimmer,
             wise
-Suggests:
 # Non-Free.
-          gmap,
-          paml,
+Suggests: gmap,
+          paml
 # Removed from Debian at all molphy,
 # Removed from Debian but might be reintroduced ensembl,
-          phylip
 # The following list of packages is not available in Debian:
 # blat,
 # cap3,

Modified: trunk/packages/bioperl-run/trunk/debian/rules
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/rules	2016-12-16 08:09:29 UTC (rev 23292)
+++ trunk/packages/bioperl-run/trunk/debian/rules	2016-12-16 09:58:28 UTC (rev 23293)
@@ -4,6 +4,9 @@
 NETWORK = --network
 endif
 
+SKIPTESTS=Glimmer2 \
+          RepeatMasker
+
 %:
 	dh $@
 
@@ -11,4 +14,8 @@
 	dh_auto_configure -- --install_scripts $(NETWORK)
 
 override_dh_auto_test:
-#	PATH=$$PATH:/usr/lib/emboss dh_auto_test
+	mkdir t.skip
+	for t in $(SKIPTESTS) ; do mv t/$${t}.t t.skip ; done
+	PATH=$$PATH:/usr/lib/emboss dh_auto_test
+	mv t.skip/* t
+	rm -rf t.skip