Attachment 164511 Details for Bug 205524 – Patch to upgrade biology/htslib to 1.3

Patch to upgrade biology/htslib to 1.3

htslib-1.3.diff (text/plain), 6.23 KB, created by cartwright on 2015-12-22 23:20:22 UTC

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Creator: cartwright

Created: 2015-12-22 23:20:22 UTC

Size: 6.23 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 403942)
>+++ Makefile	(working copy)
>@@ -2,7 +2,7 @@
> # $FreeBSD$
> 
> PORTNAME=	htslib
>-PORTVERSION=	1.2.1
>+PORTVERSION=	1.3
> CATEGORIES=	biology devel
> 
> MAINTAINER=	cartwright@asu.edu
>@@ -15,11 +15,23 @@
> USE_GITHUB=	yes
> GH_ACCOUNT=	samtools
> 
>-USES=		gmake
>+USES=		autoreconf gmake perl5 shebangfix
>+USE_PERL5=	test
> USE_LDCONFIG=	yes
>-USE_AUTOTOOLS=	autoconf
>-GNU_CONFIGURE=yes
>+GNU_CONFIGURE=	yes
>+SHEBANG_FILES=	test/compare_sam.pl test/test.pl test/test_view.pl
> 
>+OPTIONS_DEFINE=	libcurl
>+OPTIONS_DEFAULT=	libcurl
>+libcurl_DESC=	Use libcurl for network file access (HTTPS and S3 support).
>+
>+libcurl_LIB_DEPENDS=	libcurl.so:${PORTSDIR}/ftp/curl
>+
>+.include <bsd.port.options.mk>
>+
>+CPPFLAGS+=	-I${LOCALBASE}/include
>+LDFLAGS+=	-L${LOCALBASE}/lib
>+
> MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
> 		INSTALL_DATA="${INSTALL_DATA}" \
> 		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
>@@ -27,6 +39,12 @@
> 
> PLIST_SUB=	PORTVERSION="${PORTVERSION}"
> 
>+TEST_TARGET=	test
>+
>+.if ${PORT_OPTIONS:Mlibcurl}
>+CONFIGURE_ARGS+=	--enable-libcurl
>+.endif
>+
> post-patch:
> 	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
> 
>Index: distinfo
>===================================================================
>--- distinfo	(revision 403942)
>+++ distinfo	(working copy)
>@@ -1,2 +1,2 @@
>-SHA256 (samtools-htslib-1.2.1_GH0.tar.gz) = 4f67f0fc73ae86f3ed4336d8d8f6da3c12066e9cb5f142b685622dd6b8f9ae42
>-SIZE (samtools-htslib-1.2.1_GH0.tar.gz) = 997625
>+SHA256 (samtools-htslib-1.3_GH0.tar.gz) = 291a54090df3bc367b509890e1cfa34d53b1ee9be42c5fa6c2b1e2ec8f8b13af
>+SIZE (samtools-htslib-1.3_GH0.tar.gz) = 1042953
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 403991)
>+++ files/patch-Makefile	(working copy)
>@@ -1,6 +1,6 @@
>---- Makefile.orig	2015-02-03 16:22:23 UTC
>+--- Makefile.orig	2015-12-15 16:34:33 UTC
> +++ Makefile
>-@@ -22,16 +22,9 @@
>+@@ -22,16 +22,7 @@
>  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
>  # DEALINGS IN THE SOFTWARE.
>  
>@@ -8,19 +8,18 @@
> -AR     = ar
> -RANLIB = ranlib
> -
>--CPPFLAGS = -I.
>-+CPPFLAGS += -I.
>- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
>+-CPPFLAGS =
>+-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
> -CFLAGS   = -g -Wall -O2
>  EXTRA_CFLAGS_PIC = -fpic
> -LDFLAGS  =
>--LDLIBS   =
>+-LIBS     =
>  
>  # 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
>+@@ -58,16 +49,10 @@ includedir  = $(prefix)/include
>  libdir      = $(exec_prefix)/lib
>+ libexecdir  = $(exec_prefix)/libexec
>  datarootdir = $(prefix)/share
> -mandir      = $(datarootdir)/man
> +mandir      = $(prefix)/man
>@@ -35,18 +34,18 @@
> -INSTALL_DIR     = $(MKDIR_P) -m 755
> +pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
>  
>- BUILT_PROGRAMS = \
>- 	bgzip \
>-@@ -82,7 +69,7 @@ BUILT_TEST_PROGRAMS = \
>+ # Set by config.mk if plugins are enabled
>+ plugindir =
>+@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
>  	test/test-vcf-api \
>  	test/test-vcf-sweep
>  
>--all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
>-+all: lib-static lib-shared $(BUILT_PROGRAMS)
>+-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
>++all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
>  
>  HTSPREFIX =
>  include htslib_vars.mk
>-@@ -332,7 +319,7 @@ installdirs:
>+@@ -361,7 +346,7 @@ installdirs:
>  # and libhts.so.NN (used by client executables at runtime).
>  
>  install-so: libhts.so installdirs
>Index: files/patch-configure.ac
>===================================================================
>--- files/patch-configure.ac	(revision 403991)
>+++ files/patch-configure.ac	(working copy)
>@@ -1,4 +1,4 @@
>---- configure.ac.orig	2015-02-03 16:22:23 UTC
>+--- configure.ac.orig	2015-12-15 16:34:33 UTC
> +++ configure.ac
> @@ -23,7 +23,7 @@
>  # DEALINGS IN THE SOFTWARE.
>@@ -5,7 +5,7 @@
>  
>  dnl Process this file with autoconf to produce a configure script
> -AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
>-+AC_INIT([HTSlib], [@PORTVERSION@],
>++AC_INIT([HTSlib], [1.3],
>          [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)
>Index: files/patch-cram_cram__io.c
>===================================================================
>--- files/patch-cram_cram__io.c	(revision 403942)
>+++ files/patch-cram_cram__io.c	(working copy)
>@@ -1,10 +0,0 @@
>---- 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>
>Index: files/patch-hfile__libcurl.c
>===================================================================
>--- files/patch-hfile__libcurl.c	(revision 0)
>+++ files/patch-hfile__libcurl.c	(working copy)
>@@ -0,0 +1,14 @@
>+--- hfile_libcurl.c.orig	2015-12-22 22:35:42 UTC
>++++ hfile_libcurl.c
>+@@ -39,6 +39,11 @@ DEALINGS IN THE SOFTWARE.  */
>+ 
>+ #include <curl/curl.h>
>+ 
>++#include <sys/param.h>
>++#if defined(__FreeBSD__) && (__FreeBSD_version < 1000033) && !defined(ENOTRECOVERABLE)
>++#	define ENOTRECOVERABLE EIO
>++#endif
>++
>+ typedef struct {
>+     hFILE base;
>+     CURL *easy;
>
>Property changes on: files/patch-hfile__libcurl.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 403942)
>+++ pkg-plist	(working copy)
>@@ -2,10 +2,12 @@
> bin/htsfile
> bin/tabix
> include/htslib/bgzf.h
>+include/htslib/cram.h
> include/htslib/faidx.h
> include/htslib/hfile.h
> include/htslib/hts.h
> include/htslib/hts_defs.h
>+include/htslib/kbitset.h
> include/htslib/kfunc.h
> include/htslib/khash.h
> include/htslib/khash_str2int.h

Flags:

vlad-fbsd: maintainer-approval+

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Attachments on bug 205524: 164511 | 164512 | 164513