diff options
| author | Petar Petrov <petar.petrov@student.oulu.fi> | 2013-12-14 07:31:21 +0700 |
|---|---|---|
| committer | Erik Hanson <erik@slackbuilds.org> | 2013-12-14 10:53:05 -0600 |
| commit | 70013017755f78c0636a880522351dc5b588277e (patch) | |
| tree | eac41e23ff997e41eb9b813e8fed747f6d8ac8ea /academic/bowtie/patches | |
| parent | ca3a131931b1c0a9fca77630daddd3349048a569 (diff) | |
academic/bowtie: Updated for version 1.0.0.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/bowtie/patches')
4 files changed, 99 insertions, 0 deletions
diff --git a/academic/bowtie/patches/disable_bits_flag.patch b/academic/bowtie/patches/disable_bits_flag.patch new file mode 100644 index 0000000000000..3d849240e7b28 --- /dev/null +++ b/academic/bowtie/patches/disable_bits_flag.patch @@ -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 <ogi@debian.org> +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 $(BITS_FLAG) + NOASSERT_FLAGS = -DNDEBUG diff --git a/academic/bowtie/patches/no_hash_style_both_for_mips.patch b/academic/bowtie/patches/no_hash_style_both_for_mips.patch new file mode 100644 index 0000000000000..c7f8ab32e1462 --- /dev/null +++ b/academic/bowtie/patches/no_hash_style_both_for_mips.patch @@ -0,0 +1,20 @@ +Description: Disable -Wl,--hash-style=both on mips machines. + It's not supported on mips and mipsel ports and leads to build errors. +Author: Ognyan Kulev <ogi@debian.org> +Forwarded: not-needed +Last-Update: 2013-04-24 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- bowtie-1.0.0.orig/Makefile ++++ bowtie-1.0.0/Makefile +@@ -45,7 +45,9 @@ + LINUX = 0 + ifneq (,$(findstring Linux,$(shell uname))) + LINUX = 1 +- EXTRA_FLAGS += -Wl,--hash-style=both ++ ifeq (,$(findstring mips,$(shell uname -m))) ++ EXTRA_FLAGS += -Wl,--hash-style=both ++ endif + endif + + MM_DEF = diff --git a/academic/bowtie/patches/seqan-fix-setBegin-call.patch b/academic/bowtie/patches/seqan-fix-setBegin-call.patch new file mode 100644 index 0000000000000..56c8763117c90 --- /dev/null +++ b/academic/bowtie/patches/seqan-fix-setBegin-call.patch @@ -0,0 +1,42 @@ +Description: Proper type-casting in using seqan::_setBegin(). + Required by newer versions of GCC. +Forwarded: no +Author: Ognyan Kulev <ogi@debian.org> +Last-Update: 2013-04-18 + +--- a/pat.h ++++ b/pat.h +@@ -82,20 +82,20 @@ + ~ReadBuf() { + clearAll(); reset(); + // Prevent seqan from trying to free buffers +- _setBegin(patFw, NULL); +- _setBegin(patRc, NULL); +- _setBegin(qual, NULL); +- _setBegin(patFwRev, NULL); +- _setBegin(patRcRev, NULL); +- _setBegin(qualRev, NULL); +- _setBegin(name, NULL); ++ _setBegin(patFw, (Dna5*)NULL); ++ _setBegin(patRc, (Dna5*)NULL); ++ _setBegin(qual, (char*)NULL); ++ _setBegin(patFwRev, (Dna5*)NULL); ++ _setBegin(patRcRev, (Dna5*)NULL); ++ _setBegin(qualRev, (char*)NULL); ++ _setBegin(name, (char*)NULL); + for(int j = 0; j < 3; j++) { +- _setBegin(altPatFw[j], NULL); +- _setBegin(altPatFwRev[j], NULL); +- _setBegin(altPatRc[j], NULL); +- _setBegin(altPatRcRev[j], NULL); +- _setBegin(altQual[j], NULL); +- _setBegin(altQualRev[j], NULL); ++ _setBegin(altPatFw[j], (Dna5*)NULL); ++ _setBegin(altPatFwRev[j], (Dna5*)NULL); ++ _setBegin(altPatRc[j], (Dna5*)NULL); ++ _setBegin(altPatRcRev[j], (Dna5*)NULL); ++ _setBegin(altQual[j], (char*)NULL); ++ _setBegin(altQualRev[j], (char*)NULL); + } + } + diff --git a/academic/bowtie/patches/use-dpkg-buildflags.patch b/academic/bowtie/patches/use-dpkg-buildflags.patch new file mode 100644 index 0000000000000..7225d19af2c2d --- /dev/null +++ b/academic/bowtie/patches/use-dpkg-buildflags.patch @@ -0,0 +1,17 @@ +Description: Use build flags from environment (dpkg-buildflags). + Necessary for hardening flags. +Author: Simon Ruderich <simon@ruderich.org> +Last-Update: 2012-04-24 +Bug-Closed: http://bugs.debian.org/670230 + +--- a/Makefile ++++ b/Makefile +@@ -173,7 +173,7 @@ + $(MM_DEF) \ + $(SHMEM_DEF) + +-ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS) ++ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) + DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\"" + RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\"" + |