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commit 7f849394b182bc4b7925f62f40f68253c72f5bf6 Author: Andreas Tille <[email protected]> Date: Sat Jul 18 17:42:34 2015 +0200 New upstream version --- debian/changelog | 6 ++++++ debian/patches/bashism_in_shell_script.patch | 4 ++-- debian/patches/fix_build_w_seqan1.4.patch | 6 +++--- debian/patches/fix_includes_path.patch | 28 ++++++++++++++-------------- debian/patches/hardening4samtools.patch | 6 +++--- 5 files changed, 28 insertions(+), 22 deletions(-) diff --git a/debian/changelog b/debian/changelog index c52f9ac..2002ae9 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +tophat (2.1.0+dfsg-1) UNRELEASED; urgency=medium + + * New upstream version + + -- Andreas Tille <[email protected]> Sat, 18 Jul 2015 17:42:10 +0200 + tophat (2.0.14+dfsg-1) unstable; urgency=medium * Imported Upstream version 2.0.14+dfsg diff --git a/debian/patches/bashism_in_shell_script.patch b/debian/patches/bashism_in_shell_script.patch index 268dd08..5943ca8 100644 --- a/debian/patches/bashism_in_shell_script.patch +++ b/debian/patches/bashism_in_shell_script.patch @@ -1,8 +1,8 @@ Description: Remove bashism from shell script Bug-Closed: http://bugs.debian.org/671813 Author: Andreas Tille <[email protected]> ---- tophat.orig/src/tophat2.in -+++ tophat/src/tophat2.in +--- a/src/tophat2.in ++++ b/src/tophat2.in @@ -1,9 +1,9 @@ #!/bin/bash prefix="__PREFIX__" diff --git a/debian/patches/fix_build_w_seqan1.4.patch b/debian/patches/fix_build_w_seqan1.4.patch index f767aae..7ab7c5a 100644 --- a/debian/patches/fix_build_w_seqan1.4.patch +++ b/debian/patches/fix_build_w_seqan1.4.patch @@ -1,9 +1,9 @@ Description: Resolves build failure with seqan 1.4 Bug-Closed: http://bugs.debian.org/733352 Author: Manuel Holtgrewe <[email protected]> ---- tophat.orig/src/segment_juncs.cpp -+++ tophat/src/segment_juncs.cpp -@@ -2050,10 +2050,13 @@ +--- a/src/segment_juncs.cpp ++++ b/src/segment_juncs.cpp +@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl typedef map<uint32_t, IntronMotifs> MotifMap; MotifMap ims; diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch index 734c572..94ec400 100644 --- a/debian/patches/fix_includes_path.patch +++ b/debian/patches/fix_includes_path.patch @@ -1,8 +1,8 @@ Description: Fix_includes_path Subject: Corrected location for samtools .h files From: Alexandre Mestiashvili <[email protected]> ---- tophat.orig/src/align_status.h -+++ tophat/src/align_status.h +--- a/src/align_status.h ++++ b/src/align_status.h @@ -14,7 +14,7 @@ #include <cassert> #include <cstring> @@ -12,8 +12,8 @@ From: Alexandre Mestiashvili <[email protected]> #include "common.h" #include "bwt_map.h" ---- tophat.orig/src/bam2fastx.cpp -+++ tophat/src/bam2fastx.cpp +--- a/src/bam2fastx.cpp ++++ b/src/bam2fastx.cpp @@ -5,8 +5,8 @@ #include <assert.h> #include <string> @@ -25,8 +25,8 @@ From: Alexandre Mestiashvili <[email protected]> using namespace std; ---- tophat.orig/src/bwt_map.h -+++ tophat/src/bwt_map.h +--- a/src/bwt_map.h ++++ b/src/bwt_map.h @@ -16,7 +16,7 @@ #include <algorithm> #include <seqan/sequence.h> @@ -36,9 +36,9 @@ From: Alexandre Mestiashvili <[email protected]> using namespace std; #include "common.h" ---- tophat.orig/src/common.h -+++ tophat/src/common.h -@@ -15,8 +15,8 @@ +--- a/src/common.h ++++ b/src/common.h +@@ -16,8 +16,8 @@ #include <cstdio> #include <string> #include <vector> @@ -49,8 +49,8 @@ From: Alexandre Mestiashvili <[email protected]> #define MAX_READ_LEN 1024 ---- tophat.orig/src/map2gtf.h -+++ tophat/src/map2gtf.h +--- a/src/map2gtf.h ++++ b/src/map2gtf.h @@ -20,8 +20,8 @@ #include <sstream> #include <vector> @@ -62,9 +62,9 @@ From: Alexandre Mestiashvili <[email protected]> #include <seqan/sequence.h> ---- tophat.orig/configure.ac -+++ tophat/configure.ac -@@ -105,7 +105,7 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -105,7 +105,7 @@ AS_IF([test "x$enable_debug" = xyes], CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" CXXFLAGS="$CFLAGS" diff --git a/debian/patches/hardening4samtools.patch b/debian/patches/hardening4samtools.patch index cf37497..ea04e09 100644 --- a/debian/patches/hardening4samtools.patch +++ b/debian/patches/hardening4samtools.patch @@ -1,8 +1,8 @@ Description: Hardening for samtools Subject: add hardening flags to embedded copy of samtools Author: Alex Mestiashvili <[email protected]> ---- tophat.orig/src/samtools-0.1.18/Makefile -+++ tophat/src/samtools-0.1.18/Makefile +--- a/src/samtools-0.1.18/Makefile ++++ b/src/samtools-0.1.18/Makefile @@ -1,5 +1,7 @@ CC= gcc -CFLAGS= -g -Wall -O2 #-m64 #-arch ppc @@ -12,7 +12,7 @@ Author: Alex Mestiashvili <[email protected]> DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 KNETFILE_O= knetfile.o LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ -@@ -41,7 +43,7 @@ +@@ -41,7 +43,7 @@ libbam.a:$(LOBJS) $(AR) -csru $@ $(LOBJS) samtools_0.1.18:lib-recur $(AOBJS) -- 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
