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Update htslib from jb-wip
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By: outpaddling
Date: Wed May 11 09:07:28 2016 -0500
Changeset: fd27a9687e7a8d6e7a036965e42792efce83b6ce
Modified Files:
htslib/DESCR
htslib/Makefile
htslib/PLIST
htslib/buildlink3.mk
htslib/distinfo
Added Files:
htslib/TODO
htslib/patches/patch-Makefile
htslib/patches/patch-configure.ac
htslib/patches/patch-hfile__libcurl.c
Log Message:
Update htslib from jb-wip
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=fd27a9687e7a8d6e7a036965e42792efce83b6ce
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
htslib/DESCR | 13 ++-----
htslib/Makefile | 64 +++++++++++++++++++++++++++++++----
htslib/PLIST | 4 +--
htslib/TODO | 1 +
htslib/buildlink3.mk | 18 ++++++++++
htslib/distinfo | 11 +++---
htslib/patches/patch-Makefile | 58 +++++++++++++++++++++++++++++++
htslib/patches/patch-configure.ac | 13 +++++++
htslib/patches/patch-hfile__libcurl.c | 15 ++++++++
9 files changed, 173 insertions(+), 24 deletions(-)
diffs:
diff --git a/htslib/DESCR b/htslib/DESCR
index 220164d..050ad06 100644
--- a/htslib/DESCR
+++ b/htslib/DESCR
@@ -1,12 +1,3 @@
HTSlib is an implementation of a unified C library for accessing common file
-formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data,
-and is the core library used by samtools and bcftools.
-HTSlib only depends on zlib.
-It is known to be compatible with gcc, g++ and clang.
-
-HTSlib implements a generalized BAM index, with file extension .csi
-(coordinate-sorted index). The HTSlib file reader first looks for the new
-index and then for the old if the new index is absent.
-
-This project also includes the popular tabix indexer, which indexes
-both .tbi and .csi formats, and the bgzip compression utility.
+formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
+data. It is the core library used by samtools and bcftools.
diff --git a/htslib/Makefile b/htslib/Makefile
index 29466d6..deb1353 100644
--- a/htslib/Makefile
+++ b/htslib/Makefile
@@ -1,19 +1,69 @@
# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Wed May 11 08:14:16 CDT 2016 #
+###########################################################
-DISTNAME= htslib-1.3
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+# TEST_DEPENDS= bash:${PORTSDIR}/shells/bash
+# Unknown tool: USE_TOOLS= autoreconf
+#USE_LDCONFIG= yes
+#OPTIONS_DEFINE= CURL
+#OPTIONS_DEFAULT= CURL
+#CURL_DESC= Use libcurl for network file access (HTTPS and S3 support).
+# CURL_LIB_DEPENDS= libcurl.so:${PORTSDIR}/ftp/curl
+#CURL_CONFIGURE_ENABLE= libcurl
+#PLIST_SUB= PORTVERSION="${PORTVERSION}"
+#TEST_TARGET= test
+
+DISTNAME= htslib-${PORTVERSION}
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/}
-EXTRACT_SUFX= .tar.bz2
+GITHUB_PROJECT= htslib
+GITHUB_TAG= ${PORTVERSION}
-MAINTAINER= pkgsrc-users%NetBSD.org@localhost
-HOMEPAGE= https://github.com/samtools/htslib/releases/download/1.3/
+MAINTAINER= bacon4000%gmail.com@localhost
+HOMEPAGE= http://www.htslib.org/
COMMENT= C library for high-throughput sequencing data formats
-LICENSE= mit
+# LICENSE= ${WRKSRC}/LICENSE
+# Test and change if necessary.
+# MAKE_JOBS_SAFE= no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES= c c++
+USE_TOOLS+= autoconf automake autoreconf gmake perl:test
GNU_CONFIGURE= yes
-USE_TOOLS+= pkg-config gmake
+REPLACE_PERL= test/compare_sam.pl test/test.pl test/test_view.pl
+
+SUBST_CLASSES+= version
+SUBST_STAGE.version= post-patch
+SUBST_SED.version+= -e 's|@PORTVERSION@|${PORTVERSION}|g'
+SUBST_FILES.version+= ${WRKSRC}/configure.ac
+
+CPPFLAGS+= -I${LOCALBASE}/include
+
+# Check this
+MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
+ INSTALL_DATA="${INSTALL_DATA}" \
+ INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
+ INSTALL_DIR="${MKDIR}"
+
+FETCH_USING= curl
+
+PORTVERSION= 1.3
+SITE_PERL= ${PREFIX}/share
+DATADIR= ${PREFIX}/share/htslib
+DOCSDIR= ${PREFIX}/share/doc/htslib
+EXAMPLESDIR= ${PREFIX}/share/examples/htslib
-#PKGCONFIG_OVERRIDE+= htslib.pc.in
+pre-configure:
+ cd ${WRKSRC} && autoreconf
+# Convert any _DEPENDS above that have a buildlink3.mk
+# .include "../..///buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
diff --git a/htslib/PLIST b/htslib/PLIST
index a040045..04c43a1 100644
--- a/htslib/PLIST
+++ b/htslib/PLIST
@@ -6,8 +6,8 @@ include/htslib/bgzf.h
include/htslib/cram.h
include/htslib/faidx.h
include/htslib/hfile.h
-include/htslib/hts.h
include/htslib/hts_defs.h
+include/htslib/hts.h
include/htslib/kbitset.h
include/htslib/kfunc.h
include/htslib/khash.h
@@ -24,11 +24,11 @@ include/htslib/tbx.h
include/htslib/vcf.h
include/htslib/vcf_sweep.h
include/htslib/vcfutils.h
+libdata/pkgconfig/htslib.pc
lib/libhts.a
lib/libhts.so
lib/libhts.so.1
lib/libhts.so.${PKGVERSION}
-lib/pkgconfig/htslib.pc
man/man1/htsfile.1
man/man1/tabix.1
man/man5/faidx.5
diff --git a/htslib/TODO b/htslib/TODO
new file mode 100644
index 0000000..b2e3b56
--- /dev/null
+++ b/htslib/TODO
@@ -0,0 +1 @@
+Clean up and test.
diff --git a/htslib/buildlink3.mk b/htslib/buildlink3.mk
index 1d945e5..f63891f 100644
--- a/htslib/buildlink3.mk
+++ b/htslib/buildlink3.mk
@@ -1,4 +1,14 @@
# $NetBSD$
+# XXX
+# XXX This file was created automatically using createbuildlink-3.17.
+# XXX After this file has been verified as correct, the comment lines
+# XXX beginning with "XXX" should be removed. Please do not commit
+# XXX unverified buildlink3.mk files.
+# XXX
+# XXX Packages that only install static libraries or headers should
+# XXX include the following line:
+# XXX
+# XXX BUILDLINK_DEPMETHOD.htslib?= build
BUILDLINK_TREE+= htslib
@@ -7,6 +17,14 @@ HTSLIB_BUILDLINK3_MK:=
BUILDLINK_API_DEPENDS.htslib+= htslib>=1.3
BUILDLINK_PKGSRCDIR.htslib?= ../../wip/htslib
+
+# XXX
+# XXX Uncomment and keep only the buildlink3 lines below which are directly
+# XXX needed for dependencies to compile, link, and run. If this package
+# XXX provides a wrappered API or otherwise does not expose the APIs of the
+# XXX buildlink3 lines below to dependencies, remove them.
+# XXX
+#.include "../../devel/zlib/buildlink3.mk"
.endif # HTSLIB_BUILDLINK3_MK
BUILDLINK_TREE+= -htslib
diff --git a/htslib/distinfo b/htslib/distinfo
index f2cc5a4..a24851f 100644
--- a/htslib/distinfo
+++ b/htslib/distinfo
@@ -1,6 +1,9 @@
$NetBSD$
-SHA1 (htslib-1.3.tar.bz2) = 917981547952ad02e6041a6032e0cc18896b92ec
-RMD160 (htslib-1.3.tar.bz2) = 0947a319f2f9263a100902e9e065c07d79dc6be3
-SHA512 (htslib-1.3.tar.bz2) = 1a96fd22632b4a593596645b3a40aa59aaaaa9f342f97ec8c1807fe4058576420ba2c6279594d00bfc67db93aa858bd63bf3e2cf1a63e79605791c6f8aef097c
-Size (htslib-1.3.tar.bz2) = 952864 bytes
+SHA1 (htslib-1.3.tar.gz) = 356eae930da23c74c315a85d59d2a61b96d6f702
+RMD160 (htslib-1.3.tar.gz) = 6fa662ba22b5f67224e5aa6b0388e062127dda80
+SHA512 (htslib-1.3.tar.gz) = 82748d39a862582a0376e5fe27e80462c5ac55ab7f29c049c0f2f10de27f8e46ea751d5603005392886804d3048dd3ca62a6cc709c2c012de8a02b4cc6ad98fe
+Size (htslib-1.3.tar.gz) = 1042953 bytes
+SHA1 (patch-Makefile) = 73f92ba7dac13f4fd35586982d841aedfc047c51
+SHA1 (patch-configure.ac) = 0154f80956488605fc9683fd26357e87e78abcf2
+SHA1 (patch-hfile__libcurl.c) = 97853952c6fef571b511cb5e3de2869f088f2a19
diff --git a/htslib/patches/patch-Makefile b/htslib/patches/patch-Makefile
new file mode 100644
index 0000000..24df38e
--- /dev/null
+++ b/htslib/patches/patch-Makefile
@@ -0,0 +1,58 @@
+$NetBSD$
+
+--- Makefile.orig 2015-12-15 16:34:33 UTC
++++ Makefile
+@@ -22,16 +22,7 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+
+-CC = gcc
+-AR = ar
+-RANLIB = ranlib
+-
+-CPPFLAGS =
+-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+-CFLAGS = -g -Wall -O2
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS =
+-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.
+@@ -58,16 +49,10 @@ includedir = $(prefix)/include
+ libdir = $(exec_prefix)/lib
+ libexecdir = $(exec_prefix)/libexec
+ datarootdir = $(prefix)/share
+-mandir = $(datarootdir)/man
++mandir = $(prefix)/man
+ man1dir = $(mandir)/man1
+ man5dir = $(mandir)/man5
+-pkgconfigdir= $(libdir)/pkgconfig
+-
+-MKDIR_P = mkdir -p
+-INSTALL = install -p
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_DATA = $(INSTALL) -m 644
+-INSTALL_DIR = $(MKDIR_P) -m 755
++pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
+
+ # 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) plugins $(BUILT_TEST_PROGRAMS)
++all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
+
+ HTSPREFIX =
+ include htslib_vars.mk
+@@ -361,7 +346,7 @@ 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.$(LIBHTS_SOVERSION)
+
diff --git a/htslib/patches/patch-configure.ac b/htslib/patches/patch-configure.ac
new file mode 100644
index 0000000..5b35e7c
--- /dev/null
+++ b/htslib/patches/patch-configure.ac
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- 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@localhost], [], [http://www.htslib.org/])
+ AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER
+ AC_CONFIG_SRCDIR(hts.c)
diff --git a/htslib/patches/patch-hfile__libcurl.c b/htslib/patches/patch-hfile__libcurl.c
new file mode 100644
index 0000000..1fdcc0c
--- /dev/null
+++ b/htslib/patches/patch-hfile__libcurl.c
@@ -0,0 +1,15 @@
+$NetBSD$
+
+--- hfile_libcurl.c.orig 2015-12-15 16:34:33 UTC
++++ hfile_libcurl.c
+@@ -39,6 +39,10 @@ DEALINGS IN THE SOFTWARE. */
+
+ #include <curl/curl.h>
+
++#ifndef ENOTRECOVERABLE
++#define ENOTRECOVERABLE EIO
++#endif
++
+ typedef struct {
+ hFILE base;
+ CURL *easy;
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