Date: Fri, 6 Mar 2015 12:45:23 +0000 (UTC) From: Bartek Rutkowski <robak@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r380596 - in head/biology/htslib: . files Message-ID: <201503061245.t26CjNpr023804@svn.freebsd.org>
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Author: robak Date: Fri Mar 6 12:45:22 2015 New Revision: 380596 URL: https://svnweb.freebsd.org/changeset/ports/380596 QAT: https://qat.redports.org/buildarchive/r380596/ Log: biology/htslib: update 1.1 -> 1.2.1 PR: 198291 Submitted by: Reed Cartwright <cartwright@asu.edu> Added: head/biology/htslib/files/patch-configure.ac (contents, props changed) head/biology/htslib/files/patch-cram_cram__io.c (contents, props changed) Modified: head/biology/htslib/Makefile head/biology/htslib/distinfo head/biology/htslib/files/patch-Makefile head/biology/htslib/pkg-plist Modified: head/biology/htslib/Makefile ============================================================================== --- head/biology/htslib/Makefile Fri Mar 6 12:26:39 2015 (r380595) +++ head/biology/htslib/Makefile Fri Mar 6 12:45:22 2015 (r380596) @@ -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 @@ LICENSE_FILE= ${WRKSRC}/LICENSE USE_GITHUB= yes GH_ACCOUNT= samtools -GH_COMMIT= a65fba2 +GH_COMMIT= 6042ece USES= gmake USE_LDCONFIG= yes +USE_AUTOTOOLS= autoconf +GNU_CONFIGURE=yes MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \ INSTALL_DATA="${INSTALL_DATA}" \ @@ -26,4 +28,7 @@ MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \ PLIST_SUB= PORTVERSION="${PORTVERSION}" +post-patch: + @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac + .include <bsd.port.mk> Modified: head/biology/htslib/distinfo ============================================================================== --- head/biology/htslib/distinfo Fri Mar 6 12:26:39 2015 (r380595) +++ head/biology/htslib/distinfo Fri Mar 6 12:45:22 2015 (r380596) @@ -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 Modified: head/biology/htslib/files/patch-Makefile ============================================================================== --- head/biology/htslib/files/patch-Makefile Fri Mar 6 12:26:39 2015 (r380595) +++ head/biology/htslib/files/patch-Makefile Fri Mar 6 12:45:22 2015 (r380596) @@ -1,35 +1,28 @@ ---- 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. -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 Added: head/biology/htslib/files/patch-configure.ac ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/htslib/files/patch-configure.ac Fri Mar 6 12:45:22 2015 (r380596) @@ -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) Added: head/biology/htslib/files/patch-cram_cram__io.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/htslib/files/patch-cram_cram__io.c Fri Mar 6 12:45:22 2015 (r380596) @@ -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> Modified: head/biology/htslib/pkg-plist ============================================================================== --- head/biology/htslib/pkg-plist Fri Mar 6 12:26:39 2015 (r380595) +++ head/biology/htslib/pkg-plist Fri Mar 6 12:45:22 2015 (r380596) @@ -1,4 +1,5 @@ bin/bgzip +bin/htsfile bin/tabix include/htslib/bgzf.h include/htslib/faidx.h @@ -13,6 +14,7 @@ include/htslib/knetfile.h 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 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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