diff options
| author | wiedi <wiedi> | 2015-12-12 16:56:04 +0000 |
|---|---|---|
| committer | wiedi <wiedi> | 2015-12-12 16:56:04 +0000 |
| commit | 74462b02fd5319d0cd731ce9d0fc2b97d9c58525 (patch) | |
| tree | ea9cc4dcae27fe256c88c0a385fbb79b3d6d6abd /biology | |
| parent | c0bbcf9dfd16d0dee38294d7864491db1cad5912 (diff) | |
| download | pkgsrc-74462b02fd5319d0cd731ce9d0fc2b97d9c58525.tar.gz | |
Fix int types and network libs on SunOS
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/bwa/Makefile | 6 | ||||
| -rw-r--r-- | biology/bwa/distinfo | 3 | ||||
| -rw-r--r-- | biology/bwa/patches/patch-Makefile | 24 |
3 files changed, 31 insertions, 2 deletions
diff --git a/biology/bwa/Makefile b/biology/bwa/Makefile index 9a98275e953..b207b041c69 100644 --- a/biology/bwa/Makefile +++ b/biology/bwa/Makefile @@ -1,10 +1,11 @@ -# $NetBSD: Makefile,v 1.2 2015/11/07 20:20:54 dholland Exp $ +# $NetBSD: Makefile,v 1.3 2015/12/12 16:56:04 wiedi Exp $ # DISTNAME= bwa-0.7.9a CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=bio-bwa/} EXTRACT_SUFX= .tar.bz2 +PKGREVISION= 1 MAINTAINER= jwbacon@tds.net HOMEPAGE= http://bio-bwa.sourceforge.net/ @@ -19,6 +20,9 @@ INSTALLATION_DIRS= bin ${PKGMANDIR}/man1 # unconditionally uses <emmintrin.h> ONLY_FOR_PLATFORM= *-*-x86_64 *-*-i386 *-*-ia64 +CFLAGS.SunOS+= -Du_int32_t=uint32_t +LDFLAGS.SunOS+= -lsocket -lnsl + do-install: ${INSTALL_PROGRAM} ${WRKSRC}/bwa ${DESTDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${DESTDIR}${PREFIX}/bin diff --git a/biology/bwa/distinfo b/biology/bwa/distinfo index e0f3b548e0a..9bb97881f6a 100644 --- a/biology/bwa/distinfo +++ b/biology/bwa/distinfo @@ -1,6 +1,7 @@ -$NetBSD: distinfo,v 1.2 2015/11/02 18:42:20 agc Exp $ +$NetBSD: distinfo,v 1.3 2015/12/12 16:56:04 wiedi Exp $ SHA1 (bwa-0.7.9a.tar.bz2) = a77ce327e8acba554b1d27bfdd1c148f79726484 RMD160 (bwa-0.7.9a.tar.bz2) = a51b7c686a206144eab2aee0a372d5ae46fcfce1 SHA512 (bwa-0.7.9a.tar.bz2) = 93804b2c0ac0f675e76f762441e1eec039d7f1cf77b033fd88f2e6c39d9cd4b5c21bba9fb44e34a3dab28c630c3855792a707e5b33109d4be0097cec97eaa686 Size (bwa-0.7.9a.tar.bz2) = 166193 bytes +SHA1 (patch-Makefile) = 2bb665cb579d20a07ae7c2be8ba0ed874d60d5b0 diff --git a/biology/bwa/patches/patch-Makefile b/biology/bwa/patches/patch-Makefile new file mode 100644 index 00000000000..beec4b03f6e --- /dev/null +++ b/biology/bwa/patches/patch-Makefile @@ -0,0 +1,24 @@ +$NetBSD: patch-Makefile,v 1.1 2015/12/12 16:56:04 wiedi Exp $ + +Don't overwrite pkgsrc CC and CFLAGS + +--- Makefile.orig 2014-05-19 13:11:41.000000000 +0000 ++++ Makefile +@@ -1,6 +1,6 @@ +-CC= gcc ++#CC= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++#CFLAGS= -g -Wall -Wno-unused-function -O2 + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS + AR= ar + DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) +@@ -11,7 +11,7 @@ AOBJS= QSufSort.o bwt_gen.o bwase.o bwa + bwtsw2_chain.o fastmap.o bwtsw2_pair.o + PROG= bwa + INCLUDES= +-LIBS= -lm -lz -lpthread ++LIBS= -lm -lz -lpthread $(LDFLAGS) + SUBDIRS= . + + .SUFFIXES:.c .o .cc |