[med-svn] r16621 - in trunk/packages/smalt/trunk/debian: . patches

Wed Apr 9 10:02:33 UTC 2014

Author: tille
Date: 2014-04-09 10:02:33 +0000 (Wed, 09 Apr 2014)
New Revision: 16621

Added:
   trunk/packages/smalt/trunk/debian/patches/
   trunk/packages/smalt/trunk/debian/patches/bam_cigar_test_makefile.patch
   trunk/packages/smalt/trunk/debian/patches/exclude_bam_cigar_test.patch
   trunk/packages/smalt/trunk/debian/patches/series
   trunk/packages/smalt/trunk/debian/patches/try_to_fix_automake.patch
Modified:
   trunk/packages/smalt/trunk/debian/control
   trunk/packages/smalt/trunk/debian/rules
Log:
Make sure all tests that can pass will really pass; hack around an error in test/Makefile.am in debian/rules since automake is not working as expected


Modified: trunk/packages/smalt/trunk/debian/control
===================================================================

--- trunk/packages/smalt/trunk/debian/control	2014-04-08 18:57:00 UTC (rev 16620)
+++ trunk/packages/smalt/trunk/debian/control	2014-04-09 10:02:33 UTC (rev 16621)
@@ -4,7 +4,8 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
 Build-Depends: debhelper (>= 9),
-               python-biopython,
+               zlib1g-dev,
+               python,
                samtools
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/smalt/trunk/

Added: trunk/packages/smalt/trunk/debian/patches/bam_cigar_test_makefile.patch
===================================================================
--- trunk/packages/smalt/trunk/debian/patches/bam_cigar_test_makefile.patch	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/patches/bam_cigar_test_makefile.patch	2014-04-09 10:02:33 UTC (rev 16621)
@@ -0,0 +1,19 @@
+Author: Hannes Ponstingl <hp3 at sanger.ac.uk>
+Last-Update: Wed, 09 Apr 2014 10:06:18 +0100
+Description: Correctly exclude bam_cigar_test.py in absence of bambamc library
+
+--- a/test/Makefile.am
++++ b/test/Makefile.am
+@@ -89,11 +89,10 @@ TESTS += ${TEST_DRIVERS}
+ 
+ if WITH_BAMBAMC
+ TESTS += ioform_test.py xali_test.py
+-endif
+-
+ if WITH_SAMTOOLS_EXEC
+ TESTS += bam_cigar_test.py
+ endif
++endif
+ 
+ else
+ TESTS =

Added: trunk/packages/smalt/trunk/debian/patches/exclude_bam_cigar_test.patch
===================================================================
--- trunk/packages/smalt/trunk/debian/patches/exclude_bam_cigar_test.patch	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/patches/exclude_bam_cigar_test.patch	2014-04-09 10:02:33 UTC (rev 16621)
@@ -0,0 +1,43 @@
+--- a/test/Makefile.am
++++ b/test/Makefile.am
+@@ -1,4 +1,6 @@
+ ## Process this file with automake to produce Makefile.in
++AUTOMAKE_OPTIONS = subdir-objects
++
+ DIST_SUBDIRS = data
+ 
+ INCLUDE_PATTERN = -I%
+@@ -87,11 +89,11 @@ endif
+ 
+ TESTS += ${TEST_DRIVERS}
+ 
+-if WITH_BAMBAMC
++if WITH_SAMTOOLS_EXEC
+ TESTS += ioform_test.py xali_test.py
+ endif
+ 
+-if WITH_SAMTOOLS_EXEC
++if WITH_BAMBAMC
+ TESTS += bam_cigar_test.py
+ endif
+ 
+--- a/misc/Makefile.am
++++ b/misc/Makefile.am
+@@ -1,4 +1,6 @@
+ ## Process this file with automake to produce Makefile.in
++AUTOMAKE_OPTIONS = subdir-objects
++
+ AM_CFLAGS = -I../src/
+ if ICC_COMPILER
+ if ICC_MMIC
+--- a/configure.ac
++++ b/configure.ac
+@@ -35,7 +35,7 @@ AC_PROG_CC([icc gcc cc])
+ # AM_PROG_CC_C_O
+ 
+ # we use a archiver, so add support for unusual archivers
+-# AM_PROG_AR
++AM_PROG_AR
+ 
+ # find pkg-config tests
+ PKG_PROG_PKG_CONFIG

Added: trunk/packages/smalt/trunk/debian/patches/series
===================================================================
--- trunk/packages/smalt/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/patches/series	2014-04-09 10:02:33 UTC (rev 16621)
@@ -0,0 +1,2 @@
+#bam_cigar_test_makefile.patch
+#try_to_fix_automake.patch

Added: trunk/packages/smalt/trunk/debian/patches/try_to_fix_automake.patch
===================================================================
--- trunk/packages/smalt/trunk/debian/patches/try_to_fix_automake.patch	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/patches/try_to_fix_automake.patch	2014-04-09 10:02:33 UTC (rev 16621)
@@ -0,0 +1,36 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 09 Apr 2014 10:06:18 +0100
+Description: Try to fix automake stuff to effectively apply
+ bam_cigar_test_makefile.patch but failed since the generated
+ Makefile is broken and tries to call
+    python /bin/bash
+
+--- a/test/Makefile.am
++++ b/test/Makefile.am
+@@ -1,4 +1,6 @@
+ ## Process this file with automake to produce Makefile.in
++AUTOMAKE_OPTIONS = subdir-objects
++
+ DIST_SUBDIRS = data
+ 
+ INCLUDE_PATTERN = -I%
+--- a/misc/Makefile.am
++++ b/misc/Makefile.am
+@@ -1,4 +1,6 @@
+ ## Process this file with automake to produce Makefile.in
++AUTOMAKE_OPTIONS = subdir-objects
++
+ AM_CFLAGS = -I../src/
+ if ICC_COMPILER
+ if ICC_MMIC
+--- a/configure.ac
++++ b/configure.ac
+@@ -35,7 +35,7 @@ AC_PROG_CC([icc gcc cc])
+ # AM_PROG_CC_C_O
+ 
+ # we use a archiver, so add support for unusual archivers
+-# AM_PROG_AR
++AM_PROG_AR
+ 
+ # find pkg-config tests
+ PKG_PROG_PKG_CONFIG

Modified: trunk/packages/smalt/trunk/debian/rules
===================================================================
--- trunk/packages/smalt/trunk/debian/rules	2014-04-08 18:57:00 UTC (rev 16620)
+++ trunk/packages/smalt/trunk/debian/rules	2014-04-09 10:02:33 UTC (rev 16621)
@@ -16,9 +16,16 @@
 # and use what is set there.  Any hint whether dh might set variables in
 # a similar manner are welcome.
 
+# autoreconf is needed to make the patch to test/Makefile.am effective
 %:
-	dh $@
+	dh $@ # --with autoreconf
 
+# Attention: As long as we do not have bambamc library packaged for
+#            Debian this needs to be excluded
+#            The packaging of the library is planed but not yet accomplished
+override_dh_auto_configure:
+	dh_auto_configure -- --with-bambamc=no
+
 override_dh_auto_install:
 	# upstream install does install more files than needed
 
@@ -26,5 +33,10 @@
 	dh_auto_clean
 	rm -fr test/*.pyc test/tmp
 
+override_dh_auto_test:
+	# Hack around the erronuous test/Makefile.am to not do a test requiring bambamc
+	sed -i 's/bam_cigar_test\.py//' test/Makefile
+	dh_auto_test
+
 #get-orig-source:
 #	. debian/get-orig-source


