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 <[email protected]> Uploaders: Andreas Tille <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
