Attachment 153797 Details for Bug 198291 – Patch to update biology/htslib to 1.2.1

[patch] Patch to update biology/htslib to 1.2.1

htslib-1.2.1.diff (text/plain), 5.70 KB, created by cartwright on 2015-03-04 21:01:58 UTC

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Creator: cartwright

Created: 2015-03-04 21:01:58 UTC

Size: 5.70 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 380449)
>+++ Makefile	(working copy)
>@@ -2,7 +2,7 @@
> # $FreeBSD$
> 
> PORTNAME=	htslib
>-PORTVERSION=	1.1
>+PORTVERSION=	1.2.1
> CATEGORIES=	biology devel
> 
> MAINTAINER=	cartwright@asu.edu
>@@ -14,10 +14,12 @@
> 
> USE_GITHUB=	yes
> GH_ACCOUNT=	samtools
>-GH_COMMIT=	a65fba2
>+GH_COMMIT=	6042ece
> 
> USES=		gmake
> USE_LDCONFIG=	yes
>+USE_AUTOTOOLS=	autoconf
>+GNU_CONFIGURE=yes
> 
> MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
> 		INSTALL_DATA="${INSTALL_DATA}" \
>@@ -26,4 +28,7 @@
> 
> PLIST_SUB=	PORTVERSION="${PORTVERSION}"
> 
>+post-patch:
>+	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
>+
> .include <bsd.port.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 380449)
>+++ distinfo	(working copy)
>@@ -1,2 +1,2 @@
>-SHA256 (htslib-1.1.tar.gz) = 0614de1795284181675dd0178fb00f0aca176064b6263e3c7e21b53f34710631
>-SIZE (htslib-1.1.tar.gz) = 957434
>+SHA256 (htslib-1.2.1.tar.gz) = 6403e84e31d3a8179405c4587118144d337b29fa215c0d2948c1c0a6099c5e58
>+SIZE (htslib-1.2.1.tar.gz) = 997746
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 380449)
>+++ files/patch-Makefile	(working copy)
>@@ -1,6 +1,6 @@
>---- Makefile.orig	2014-09-23 14:39:41 UTC
>+--- Makefile.orig	2015-02-03 16:22:23 UTC
> +++ Makefile
>-@@ -22,33 +22,27 @@
>+@@ -22,16 +22,9 @@
>  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
>  # DEALINGS IN THE SOFTWARE.
>  
>@@ -7,29 +7,22 @@
> -CC     = gcc
> -AR     = ar
> -RANLIB = ranlib
>-+CC    ?= cc
>-+AR     = /usr/bin/ar
>-+RANLIB = /usr/bin/ranlib
>- 
>- # TODO: edit cram code to remove need for -DSAMTOOLS
>--CPPFLAGS = -I. -DSAMTOOLS=1
>-+CPPFLAGS += -I. -DSAMTOOLS=1 -Wno-unused-function -Wno-implicit-function-declaration
>+-
>+-CPPFLAGS = -I.
>++CPPFLAGS += -I.
>  # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
> -CFLAGS   = -g -Wall -O2
>-+CFLAGS   += -Wall
>  EXTRA_CFLAGS_PIC = -fpic
> -LDFLAGS  =
> -LDLIBS   =
>-+LDFLAGS  +=
>-+LDLIBS   +=
>  
>--prefix      = /usr/local
>-+prefix      = ${STAGEDIR}${PREFIX}
>- exec_prefix = $(prefix)
>- bindir      = $(exec_prefix)/bin
>+ # For now these don't work too well as samtools also needs to know to
>+ # add -lbz2 and -llzma if linking against the static libhts.a library.
>+@@ -57,16 +50,10 @@ bindir      = $(exec_prefix)/bin
>  includedir  = $(prefix)/include
>  libdir      = $(exec_prefix)/lib
>--mandir      = $(prefix)/share/man
>+ datarootdir = $(prefix)/share
>+-mandir      = $(datarootdir)/man
> +mandir      = $(prefix)/man
>  man1dir     = $(mandir)/man1
>  man5dir     = $(mandir)/man5
>@@ -44,7 +37,7 @@
>  
>  BUILT_PROGRAMS = \
>  	bgzip \
>-@@ -62,7 +56,7 @@ BUILT_TEST_PROGRAMS = \
>+@@ -82,7 +69,7 @@ BUILT_TEST_PROGRAMS = \
>  	test/test-vcf-api \
>  	test/test-vcf-sweep
>  
>@@ -53,7 +46,7 @@
>  
>  HTSPREFIX =
>  include htslib_vars.mk
>-@@ -284,7 +278,7 @@ installdirs:
>+@@ -332,7 +319,7 @@ installdirs:
>  # and libhts.so.NN (used by client executables at runtime).
>  
>  install-so: libhts.so installdirs
>
>Property changes on: files/patch-Makefile
>___________________________________________________________________
>Modified: fbsd:nokeywords
>## -1 +1 ##
>-on
>\ No newline at end of property
>+yes
>\ No newline at end of property
>Index: files/patch-configure.ac
>===================================================================
>--- files/patch-configure.ac	(revision 0)
>+++ files/patch-configure.ac	(working copy)
>@@ -0,0 +1,11 @@
>+--- configure.ac.orig	2015-02-03 16:22:23 UTC
>++++ configure.ac
>+@@ -23,7 +23,7 @@
>+ # DEALINGS IN THE SOFTWARE.
>+ 
>+ dnl Process this file with autoconf to produce a configure script
>+-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
>++AC_INIT([HTSlib], [@PORTVERSION@],
>+         [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
>+ AC_PREREQ(2.63)  dnl This version introduced 4-argument AC_CHECK_HEADER
>+ AC_CONFIG_SRCDIR(hts.c)
>
>Property changes on: files/patch-configure.ac
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-cram_cram__io.c
>===================================================================
>--- files/patch-cram_cram__io.c	(revision 0)
>+++ files/patch-cram_cram__io.c	(working copy)
>@@ -0,0 +1,10 @@
>+--- cram/cram_io.c.orig	2015-02-03 16:22:23 UTC
>++++ cram/cram_io.c
>+@@ -53,6 +53,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE
>+ #include <assert.h>
>+ #include <stdlib.h>
>+ #include <string.h>
>++#include <unistd.h>
>+ #include <zlib.h>
>+ #ifdef HAVE_LIBBZ2
>+ #include <bzlib.h>
>
>Property changes on: files/patch-cram_cram__io.c
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 380449)
>+++ pkg-plist	(working copy)
>@@ -1,4 +1,5 @@
> bin/bgzip
>+bin/htsfile
> bin/tabix
> include/htslib/bgzf.h
> include/htslib/faidx.h
>@@ -13,6 +14,7 @@
> include/htslib/kseq.h
> include/htslib/ksort.h
> include/htslib/kstring.h
>+include/htslib/regidx.h
> include/htslib/sam.h
> include/htslib/synced_bcf_reader.h
> include/htslib/tbx.h
>@@ -24,6 +26,7 @@
> lib/libhts.so.1
> lib/libhts.so.%%PORTVERSION%%
> libdata/pkgconfig/htslib.pc
>+man/man1/htsfile.1.gz
> man/man1/tabix.1.gz
> man/man5/faidx.5.gz
> man/man5/sam.5.gz

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Attachments on bug 198291: 153797 | 153848 | 153849