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commit 9fbdf45147940c4b9862e868a9b014aea3d52313 Author: Alexandre Mestiashvili <[email protected]> Date: Mon Jul 7 13:27:42 2014 +0200 d/patches: updated debian/patches/fix_includes_path.patch to exclude SeqAn-1.3 from configure.ac d/control: new Homepage d/copyright: new Source --- debian/changelog | 9 +++++---- debian/control | 2 +- debian/copyright | 4 ++-- .../{fix4seqan1.4.patch => fix_build_w_seqan1.4.patch} | 0 debian/patches/fix_includes_path.patch | 11 +++++++++++ debian/patches/series | 2 +- 6 files changed, 20 insertions(+), 8 deletions(-) diff --git a/debian/changelog b/debian/changelog index 84313e3..9bc6bde 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,11 +1,12 @@ tophat (2.0.12+dfsg-1) UNRELEASED; urgency=medium - [ Andreas Tille ] - * Commit Diane's patch - [ Alexandre Mestiashvili ] - * d/watch: new url + * d/watch: new url * Imported Upstream version 2.0.12+dfsg + * d/patches/fix_build_w_seqan1.4.patch: patch from Manuel Holtgrewe resolving #733352. + removed const_ness_part1.patch as the new patch solves the problem completely + Closes: #733352 + * debian/patches/fix_includes_path.patch: exclude SeqAn-1.3 from configure.ac -- Alexandre Mestiashvili <[email protected]> Thu, 03 Jul 2014 21:06:10 +0200 diff --git a/debian/control b/debian/control index 9ad56ab..4372394 100644 --- a/debian/control +++ b/debian/control @@ -18,7 +18,7 @@ Build-Depends: debhelper (>= 9), Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/tophat.git Vcs-Git: git://anonscm.debian.org/debian-med/tophat.git -Homepage: http://tophat.cbcb.umd.edu/ +Homepage: http://ccb.jhu.edu/software/tophat Package: tophat Architecture: any diff --git a/debian/copyright b/debian/copyright index 33fc0f6..1109e44 100644 --- a/debian/copyright +++ b/debian/copyright @@ -1,7 +1,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: TopHat Upstream-Contact: Daehwan Kim <[email protected]> -Source: http://tophat.cbcb.umd.edu/downloads/tophat-2.0.10.tar.gz +Source: http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.12.tar.gz Comment: Cole Trapnell wrote TopHat. TopHat is built on Bowtie, which was written by Ben Langmead and Cole Trapnell. Daehwan Kim and Geo Pertea added support @@ -90,7 +90,7 @@ License: Files: debian/* Copyright: © 2011 Carlos Borroto <[email protected]> - © 2013 Alex Mestiashvili <[email protected]> + © 2014 Alex Mestiashvili <[email protected]> License: GPL-2+ License: GAP diff --git a/debian/patches/fix4seqan1.4.patch b/debian/patches/fix_build_w_seqan1.4.patch similarity index 100% rename from debian/patches/fix4seqan1.4.patch rename to debian/patches/fix_build_w_seqan1.4.patch diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch index 337b5c2..87c44f8 100644 --- a/debian/patches/fix_includes_path.patch +++ b/debian/patches/fix_includes_path.patch @@ -74,3 +74,14 @@ Subject: Corrected location for samtools .h files ]], [[ ]])],[ AC_MSG_RESULT(yes) +--- tophat.orig/configure.ac ++++ tophat/configure.ac +@@ -93,7 +93,7 @@ + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" + CXXFLAGS="$CFLAGS" +-CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3" ++CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS" + LDFLAGS="$user_LDFLAGS" + + AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) diff --git a/debian/patches/series b/debian/patches/series index 2ef3aff..d51df39 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,3 @@ -fix4seqan1.4.patch +fix_build_w_seqan1.4.patch fix_includes_path.patch bashism_in_shell_script.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/tophat.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
