Author: ogi Date: 2013-04-24 08:00:53 +0000 (Wed, 24 Apr 2013) New Revision: 13388
Added: trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch Modified: trunk/packages/bowtie/trunk/debian/README.source trunk/packages/bowtie/trunk/debian/changelog trunk/packages/bowtie/trunk/debian/control trunk/packages/bowtie/trunk/debian/patches/series Log: Depends on version 1.3 of SeqAn. Updated README.source. Removed machine bits detection. Modified: trunk/packages/bowtie/trunk/debian/README.source =================================================================== --- trunk/packages/bowtie/trunk/debian/README.source 2013-04-24 06:30:34 UTC (rev 13387) +++ trunk/packages/bowtie/trunk/debian/README.source 2013-04-24 08:00:53 UTC (rev 13388) @@ -1,12 +1,12 @@ bowtie for Debian ----------------- -The bowtie package seems to rely on version 1.1 of the seqan library, -while Debian otherwise already features version 1.2. It yet remains -to be investigated, to what degree the two might possibly be -compatible. +The bowtie upstream source includes version 1.1 of SeqAn library and +uses it in compilation. This Debian package changes build process and +updates bowtie's source so that Debian's seqan package is used. If you +believe this leads to problems, please inform Debian maintainer or +Debian-Med team. -We did not dare any respective experiments and hope for a clarification -by upstream on this issue - we just should not introduce any hidden -mistakes here. - +Bowtie build process have ability to select 32 or 64 bit version. This +is disabled and it is expected that users will use multiarch abilities +of Debian for choosing between running 32-bit or 64-bit version. Modified: trunk/packages/bowtie/trunk/debian/changelog =================================================================== --- trunk/packages/bowtie/trunk/debian/changelog 2013-04-24 06:30:34 UTC (rev 13387) +++ trunk/packages/bowtie/trunk/debian/changelog 2013-04-24 08:00:53 UTC (rev 13388) @@ -1,3 +1,11 @@ +bowtie (1.0.0-2) UNRELEASED; urgency=low + + * Requires version 1.3 of SeqAn. + * Updated README.source about using Debian's SeqAn library. + * Removed machine_bits_detection.patch and added disable_bits_flag.patch. + + -- Ognyan Kulev <[email protected]> Wed, 24 Apr 2013 10:49:47 +0300 + bowtie (1.0.0-1) unstable; urgency=low * New upstream version. (Closes: #705616) Modified: trunk/packages/bowtie/trunk/debian/control =================================================================== --- trunk/packages/bowtie/trunk/debian/control 2013-04-24 06:30:34 UTC (rev 13387) +++ trunk/packages/bowtie/trunk/debian/control 2013-04-24 08:00:53 UTC (rev 13388) @@ -7,7 +7,7 @@ Yask Gupta <[email protected]>, Andreas Tille <[email protected]>, Ognyan Kulev <[email protected]> -Build-Depends: debhelper (>= 9), help2man, seqan-dev +Build-Depends: debhelper (>= 9), help2man, seqan-dev (>= 1.3) Standards-Version: 3.9.3 Homepage: http://bowtie-bio.sourceforge.net/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bowtie/trunk Added: trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch (rev 0) +++ trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch 2013-04-24 08:00:53 UTC (rev 13388) @@ -0,0 +1,20 @@ +Description: Disable architecture bits detection. + In Debian, you can use multiarch facilities for choosing which version + to run. +Author: Ognyan Kulev <[email protected]> +Forwarded: not-needed +Last-Update: 2013-04-24 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- bowtie-1.0.0.orig/Makefile ++++ bowtie-1.0.0/Makefile +@@ -121,6 +121,9 @@ + BITS_FLAG = -m64 + endif + ++# Debian: Disable selection of 32/64-bits. Use multiarch instead. ++BITS_FLAG = ++ + DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) + RELEASE_FLAGS = -O3 $(BITS_FLAG) + NOASSERT_FLAGS = -DNDEBUG Modified: trunk/packages/bowtie/trunk/debian/patches/series =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/series 2013-04-24 06:30:34 UTC (rev 13387) +++ trunk/packages/bowtie/trunk/debian/patches/series 2013-04-24 08:00:53 UTC (rev 13388) @@ -3,4 +3,4 @@ seqan-fix-setBegin-call.patch seqan-rename-ChunkPool.patch seqan-rename-fill-to-resize.patch -machine_bits_detection.patch +disable_bits_flag.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
