Attachment 187279 Details for Bug 223094 – svn diff for biology/htslib

[patch] svn diff for biology/htslib

htslib-1.6.diff (text/plain), 6.14 KB, created by Motomichi Matsuzaki on 2017-10-18 14:04:24 UTC

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Creator: Motomichi Matsuzaki

Created: 2017-10-18 14:04:24 UTC

Size: 6.14 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 452329)
>+++ Makefile	(working copy)
>@@ -2,7 +2,7 @@
> # $FreeBSD$
> 
> PORTNAME=	htslib
>-PORTVERSION=	1.3.1
>+PORTVERSION=	1.6
> CATEGORIES=	biology devel
> 
> MAINTAINER=	cartwright@asu.edu
>@@ -34,16 +34,8 @@
> CPPFLAGS+=	-I${LOCALBASE}/include
> LDFLAGS+=	-L${LOCALBASE}/lib
> 
>-MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
>-		INSTALL_DATA="${INSTALL_DATA}" \
>-		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
>-		INSTALL_DIR="${MKDIR}"
>-
> PLIST_SUB=	PORTVERSION="${PORTVERSION}"
> 
> TEST_TARGET=	test
> 
>-post-patch:
>-	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
>-
> .include <bsd.port.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 452329)
>+++ distinfo	(working copy)
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1463688817
>-SHA256 (samtools-htslib-1.3.1_GH0.tar.gz) = 3bbd04f9a0c4c301abd5d19a81920894ac2ee5e86e8aa977e8c2035e01d93ea7
>-SIZE (samtools-htslib-1.3.1_GH0.tar.gz) = 1065840
>+TIMESTAMP = 1508301522
>+SHA256 (samtools-htslib-1.6_GH0.tar.gz) = 4215c9153c27603cbaaf542f2ec128c5e839380d6df6edd4dbf67955170740c6
>+SIZE (samtools-htslib-1.6_GH0.tar.gz) = 1155672
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 452329)
>+++ files/patch-Makefile	(working copy)
>@@ -1,6 +1,6 @@
>---- Makefile.orig	2016-04-22 08:45:12 UTC
>+--- Makefile.orig	2017-10-18 08:03:33 UTC
> +++ Makefile
>-@@ -22,16 +22,7 @@
>+@@ -22,41 +22,26 @@
>  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
>  # DEALINGS IN THE SOFTWARE.
>  
>@@ -8,16 +8,23 @@
> -AR     = ar
> -RANLIB = ranlib
> -
>+-# Default libraries to link if configure is not used
>+-htslib_default_libs = -lz -lm -lbz2 -llzma
>+-
> -CPPFLAGS =
> -# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
>+-# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
>+-#CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
> -CFLAGS   = -g -Wall -O2
>  EXTRA_CFLAGS_PIC = -fpic
> -LDFLAGS  =
>--LIBS     =
>+-LIBS     = $(htslib_default_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.
>-@@ -58,17 +49,11 @@ includedir  = $(prefix)/include
>+-prefix      = /usr/local
>++prefix      = ${PREFIX}
>+ exec_prefix = $(prefix)
>+ bindir      = $(exec_prefix)/bin
>+ includedir  = $(prefix)/include
>  libdir      = $(exec_prefix)/lib
>  libexecdir  = $(exec_prefix)/libexec
>  datarootdir = $(prefix)/share
>@@ -27,30 +34,27 @@
>  man5dir     = $(mandir)/man5
>  pkgconfigdir= $(prefix)/libdata/pkgconfig
>  
>--MKDIR_P = mkdir -p
>+ MKDIR_P = mkdir -p
> -INSTALL = install -p
>--INSTALL_PROGRAM = $(INSTALL)
> -INSTALL_DATA    = $(INSTALL) -m 644
> -INSTALL_DIR     = $(MKDIR_P) -m 755
>--
>+-INSTALL_LIB     = $(INSTALL_DATA)
>+-INSTALL_MAN     = $(INSTALL_DATA)
>+-INSTALL_PROGRAM = $(INSTALL)
>++INSTALL_DATA    = ${BSD_INSTALL_DATA}
>++INSTALL_DIR     = $(MKDIR_P)
>++INSTALL_LIB     = ${BSD_INSTALL_LIB}
>++INSTALL_MAN     = ${BSD_INSTALL_MAN}
>++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
>+ 
>  # Set by config.mk if plugins are enabled
>  plugindir =
>+@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \
>+ 	test/thrash_threads5 \
>+ 	test/thrash_threads6
>  
>-@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
>- 	test/test-vcf-api \
>- 	test/test-vcf-sweep
>- 
> -all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
> +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
>  
>  HTSPREFIX =
>  include htslib_vars.mk
>-@@ -360,7 +345,7 @@ installdirs:
>- # and libhts.so.NN (used by client executables at runtime).
>- 
>- install-so: libhts.so installdirs
>--	$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
>-+	$(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
>- 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
>- 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
>- 
>Index: files/patch-configure.ac
>===================================================================
>--- files/patch-configure.ac	(revision 452329)
>+++ files/patch-configure.ac	(working copy)
>@@ -1,11 +0,0 @@
>---- configure.ac.orig	2015-12-15 16:34:33 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], [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-hfile__libcurl.c
>===================================================================
>--- files/patch-hfile__libcurl.c	(revision 452329)
>+++ files/patch-hfile__libcurl.c	(working copy)
>@@ -1,13 +1,13 @@
>---- hfile_libcurl.c.orig	2015-12-15 16:34:33 UTC
>+--- hfile_libcurl.c.orig	2017-09-28 11:20:23 UTC
> +++ hfile_libcurl.c
>-@@ -39,6 +39,10 @@ DEALINGS IN THE SOFTWARE.  */
>+@@ -49,6 +49,10 @@ typedef struct {
>+     unsigned int size;
>+ } hdrlist;
>  
>- #include <curl/curl.h>
>- 
> +#ifndef ENOTRECOVERABLE
> +#define ENOTRECOVERABLE EIO
> +#endif
> +
>  typedef struct {
>-     hFILE base;
>-     CURL *easy;
>+     hdrlist fixed;                   // List of headers supplied at hopen()
>+     hdrlist extra;                   // List of headers from callback
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 452329)
>+++ pkg-plist	(working copy)
>@@ -7,6 +7,9 @@
> include/htslib/hfile.h
> include/htslib/hts.h
> include/htslib/hts_defs.h
>+include/htslib/hts_endian.h
>+include/htslib/hts_log.h
>+include/htslib/hts_os.h
> include/htslib/kbitset.h
> include/htslib/kfunc.h
> include/htslib/khash.h
>@@ -20,13 +23,14 @@
> include/htslib/sam.h
> include/htslib/synced_bcf_reader.h
> include/htslib/tbx.h
>+include/htslib/thread_pool.h
> include/htslib/vcf.h
> include/htslib/vcf_sweep.h
> include/htslib/vcfutils.h
> lib/libhts.a
> lib/libhts.so
>-lib/libhts.so.1
> lib/libhts.so.%%PORTVERSION%%
>+lib/libhts.so.2
> libdata/pkgconfig/htslib.pc
> man/man1/htsfile.1.gz
> man/man1/tabix.1.gz

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Attachments on bug 223094: 187279 | 187280 | 187281