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CVS commit: pkgsrc/biology/htslib
Module Name: pkgsrc
Committed By: bacon
Date: Wed Jul 22 14:50:14 UTC 2020
Modified Files:
pkgsrc/biology/htslib: Makefile PLIST buildlink3.mk distinfo
Added Files:
pkgsrc/biology/htslib/patches: patch-Makefile
patch-cram_open__trace__file.c patch-hfile__libcurl.c
Log Message:
biology/htslib: Upgrade to 1.10.2
Numerous enhancements and bug fixes since 1.9, including:
Elimited refernce file size limits
SAM header API
On-the-fly indexing
Improved Amazon S3 interface
This package contains a patch for recent libcurl not in the upstream release
To generate a diff of this commit:
cvs rdiff -u -r1.15 -r1.16 pkgsrc/biology/htslib/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/htslib/PLIST
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/htslib/buildlink3.mk \
pkgsrc/biology/htslib/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/htslib/patches/patch-Makefile \
pkgsrc/biology/htslib/patches/patch-cram_open__trace__file.c \
pkgsrc/biology/htslib/patches/patch-hfile__libcurl.c
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Modified files:
Index: pkgsrc/biology/htslib/Makefile
diff -u pkgsrc/biology/htslib/Makefile:1.15 pkgsrc/biology/htslib/Makefile:1.16
--- pkgsrc/biology/htslib/Makefile:1.15 Fri May 22 10:55:57 2020
+++ pkgsrc/biology/htslib/Makefile Wed Jul 22 14:50:14 2020
@@ -1,25 +1,30 @@
-# $NetBSD: Makefile,v 1.15 2020/05/22 10:55:57 adam Exp $
+# $NetBSD: Makefile,v 1.16 2020/07/22 14:50:14 bacon Exp $
-DISTNAME= htslib-1.9
-PKGREVISION= 10
+DISTNAME= htslib-1.10.2
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/}
-EXTRACT_SUFX= .tar.bz2
-GITHUB_RELEASE= ${PKGVERSION_NOREV}
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://www.htslib.org/
COMMENT= C library for high-throughput sequencing data formats
LICENSE= mit
-USE_TOOLS+= gmake perl
+USE_TOOLS+= autoconf automake autoreconf bash gmake perl
GNU_CONFIGURE= yes
+
+SUBST_CLASSES+= version
+SUBST_STAGE.version= pre-configure
+SUBST_SED.version= -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version= configure.ac
+
+REPLACE_PERL+= test/*.pl
+
CONFIGURE_ARGS+= --enable-libcurl
PKGCONFIG_OVERRIDE= htslib.pc.in
TEST_TARGET= test
-REPLACE_PERL+= test/compare_sam.pl
-REPLACE_PERL+= test/test.pl
+pre-configure:
+ cd ${WRKSRC} && autoreconf
.include "../../archivers/bzip2/buildlink3.mk"
.include "../../archivers/xz/buildlink3.mk"
Index: pkgsrc/biology/htslib/PLIST
diff -u pkgsrc/biology/htslib/PLIST:1.1 pkgsrc/biology/htslib/PLIST:1.2
--- pkgsrc/biology/htslib/PLIST:1.1 Mon Apr 30 16:51:54 2018
+++ pkgsrc/biology/htslib/PLIST Wed Jul 22 14:50:14 2020
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2018/04/30 16:51:54 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2020/07/22 14:50:14 bacon Exp $
bin/bgzip
bin/htsfile
bin/tabix
@@ -31,7 +31,7 @@ include/htslib/vcfutils.h
lib/libhts.a
lib/libhts.so
lib/libhts.so.${PKGVERSION}
-lib/libhts.so.2
+lib/libhts.so.3
lib/pkgconfig/htslib.pc
man/man1/bgzip.1
man/man1/htsfile.1
@@ -39,3 +39,4 @@ man/man1/tabix.1
man/man5/faidx.5
man/man5/sam.5
man/man5/vcf.5
+man/man7/htslib-s3-plugin.7
Index: pkgsrc/biology/htslib/buildlink3.mk
diff -u pkgsrc/biology/htslib/buildlink3.mk:1.2 pkgsrc/biology/htslib/buildlink3.mk:1.3
--- pkgsrc/biology/htslib/buildlink3.mk:1.2 Tue May 1 13:20:44 2018
+++ pkgsrc/biology/htslib/buildlink3.mk Wed Jul 22 14:50:14 2020
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.2 2018/05/01 13:20:44 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.3 2020/07/22 14:50:14 bacon Exp $
BUILDLINK_TREE+= htslib
.if !defined(HTSLIB_BUILDLINK3_MK)
HTSLIB_BUILDLINK3_MK:=
-BUILDLINK_API_DEPENDS.htslib+= htslib>=1.8
+BUILDLINK_API_DEPENDS.htslib+= htslib>=1.10.2
BUILDLINK_PKGSRCDIR.htslib?= ../../biology/htslib
.endif # HTSLIB_BUILDLINK3_MK
Index: pkgsrc/biology/htslib/distinfo
diff -u pkgsrc/biology/htslib/distinfo:1.2 pkgsrc/biology/htslib/distinfo:1.3
--- pkgsrc/biology/htslib/distinfo:1.2 Tue Nov 6 10:24:14 2018
+++ pkgsrc/biology/htslib/distinfo Wed Jul 22 14:50:14 2020
@@ -1,6 +1,9 @@
-$NetBSD: distinfo,v 1.2 2018/11/06 10:24:14 adam Exp $
+$NetBSD: distinfo,v 1.3 2020/07/22 14:50:14 bacon Exp $
-SHA1 (htslib-1.9.tar.bz2) = 21be5187203df30637dda2e1133cae2e833ef050
-RMD160 (htslib-1.9.tar.bz2) = 85d5211cc197931e73a0dc7ca0673426f2ff6d89
-SHA512 (htslib-1.9.tar.bz2) = ddb0e2d970e4c2c27e203b064898f95cb7c187cd497c02fc7b4312dcea25669d0b6063d537687521e7a065f6daefa1ae897add2df4981037a187b499d08fdef7
-Size (htslib-1.9.tar.bz2) = 1178859 bytes
+SHA1 (htslib-1.10.2.tar.gz) = 0ac4b86e49556d7dcaa89d4cce2661c9ca706631
+RMD160 (htslib-1.10.2.tar.gz) = 6d8b6a362297345420dc9acc544029276ce4b1b6
+SHA512 (htslib-1.10.2.tar.gz) = 7a91c15ca1de35653d068dc57ae511ad791ae0bd8504867d4e60c46e813e58b441409541197cde3b2a37840e60331336aebc627ecbf5c64fca1af63dd05f8f9e
+Size (htslib-1.10.2.tar.gz) = 1452177 bytes
+SHA1 (patch-Makefile) = e13333dd97ecd6c6753d14c1b738d6e5934a2911
+SHA1 (patch-cram_open__trace__file.c) = 49b47e13786317e652a8ec810cc91f10d21bb8ea
+SHA1 (patch-hfile__libcurl.c) = 2a143818f1099ef01c57a3c904060a76abb63f14
Added files:
Index: pkgsrc/biology/htslib/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/htslib/patches/patch-Makefile:1.1
--- /dev/null Wed Jul 22 14:50:14 2020
+++ pkgsrc/biology/htslib/patches/patch-Makefile Wed Jul 22 14:50:14 2020
@@ -0,0 +1,76 @@
+$NetBSD: patch-Makefile,v 1.1 2020/07/22 14:50:14 bacon Exp $
+
+# Respect pkgsrc env
+
+--- Makefile.orig 2019-12-19 09:54:30.000000000 +0000
++++ Makefile
+@@ -22,44 +22,43 @@
+ # 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 ?= gcc
++AR ?= ar
++RANLIB ?= ranlib
+
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl
+
+-CPPFLAGS =
++# CPPFLAGS =
+ # TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64
+ # to CFLAGS manually, here or in config.mk if the latter exists.
+ # 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
+-CFLAGS = -g -Wall -O2 -fvisibility=hidden
++CFLAGS ?= -g -Wall -O2 -fvisibility=hidden
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS = -fvisibility=hidden
++LDFLAGS ?= -fvisibility=hidden
+ LIBS = $(htslib_default_libs)
+
+-prefix = /usr/local
+-exec_prefix = $(prefix)
++PREFIX ?= /usr/local
++exec_prefix = $(PREFIX)
+ bindir = $(exec_prefix)/bin
+-includedir = $(prefix)/include
++includedir = $(PREFIX)/include
+ libdir = $(exec_prefix)/lib
+ libexecdir = $(exec_prefix)/libexec
+-datarootdir = $(prefix)/share
++datarootdir = $(PREFIX)/share
+ mandir = $(datarootdir)/man
+ man1dir = $(mandir)/man1
+ man5dir = $(mandir)/man5
+ man7dir = $(mandir)/man7
+ pkgconfigdir= $(libdir)/pkgconfig
+
+-MKDIR_P = mkdir -p
+-INSTALL = install -p
+-INSTALL_DATA = $(INSTALL) -m 644
+-INSTALL_DIR = $(MKDIR_P) -m 755
+-INSTALL_LIB = $(INSTALL_DATA)
+-INSTALL_MAN = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
++MKDIR_P = mkdir -p
++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 =
+@@ -98,7 +97,7 @@ BUILT_THRASH_PROGRAMS = \
+ test/thrash_threads6 \
+ test/thrash_threads7
+
+-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
++all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
+
+ HTSPREFIX =
+ include htslib_vars.mk
Index: pkgsrc/biology/htslib/patches/patch-cram_open__trace__file.c
diff -u /dev/null pkgsrc/biology/htslib/patches/patch-cram_open__trace__file.c:1.1
--- /dev/null Wed Jul 22 14:50:14 2020
+++ pkgsrc/biology/htslib/patches/patch-cram_open__trace__file.c Wed Jul 22 14:50:14 2020
@@ -0,0 +1,18 @@
+$NetBSD: patch-cram_open__trace__file.c,v 1.1 2020/07/22 14:50:14 bacon Exp $
+
+# Enhance error message
+
+--- cram/open_trace_file.c.orig 2019-12-19 09:54:30.000000000 +0000
++++ cram/open_trace_file.c
+@@ -204,8 +204,9 @@ mFILE *find_file_url(const char *file, c
+ goto fail;
+ }
+ }
+- if (hclose(hf) < 0 || len < 0) {
+- hts_log_warning("Failed to read reference \"%s\": %s", path, strerror(errno));
++ int close_status = hclose(hf);
++ if (close_status < 0 || len < 0) {
++ hts_log_warning("Failed to read reference \"%s\": %s close_status = %d len = %ld", path, strerror(errno));
+ goto fail;
+ }
+
Index: pkgsrc/biology/htslib/patches/patch-hfile__libcurl.c
diff -u /dev/null pkgsrc/biology/htslib/patches/patch-hfile__libcurl.c:1.1
--- /dev/null Wed Jul 22 14:50:14 2020
+++ pkgsrc/biology/htslib/patches/patch-hfile__libcurl.c Wed Jul 22 14:50:14 2020
@@ -0,0 +1,78 @@
+$NetBSD: patch-hfile__libcurl.c,v 1.1 2020/07/22 14:50:14 bacon Exp $
+
+# recent libcurl compatibility
+
+--- hfile_libcurl.c.orig 2019-12-19 09:54:30.000000000 +0000
++++ hfile_libcurl.c
+@@ -74,6 +74,10 @@ typedef struct {
+ unsigned int size;
+ } hdrlist;
+
++#ifndef ENOTRECOVERABLE
++#define ENOTRECOVERABLE EIO
++#endif
++
+ typedef struct {
+ hdrlist fixed; // List of headers supplied at hopen()
+ hdrlist extra; // List of headers from callback
+@@ -218,6 +222,8 @@ static int easy_errno(CURL *easy, CURLco
+ return EEXIST;
+
+ default:
++ hts_log_error("Libcurl reported error %d (%s)", (int) err,
++ curl_easy_strerror(err));
+ return EIO;
+ }
+ }
+@@ -238,6 +244,8 @@ static int multi_errno(CURLMcode errm)
+ return ENOMEM;
+
+ default:
++ hts_log_error("Libcurl reported error %d (%s)", (int) errm,
++ curl_multi_strerror(errm));
+ return EIO;
+ }
+ }
+@@ -797,9 +805,13 @@ static ssize_t libcurl_read(hFILE *fpv,
+ fp->buffer.ptr.rd = buffer;
+ fp->buffer.len = nbytes;
+ fp->paused = 0;
+- err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
+- if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; }
+-
++ if (! fp->finished) {
++ err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
++ if (err != CURLE_OK) {
++ errno = easy_errno(fp->easy, err);
++ return -1;
++ }
++ }
+ while (! fp->paused && ! fp->finished) {
+ if (wait_perform(fp) < 0) return -1;
+ }
+@@ -1003,12 +1015,6 @@ static int restart_from_position(hFILE_l
+ }
+ temp_fp.nrunning = ++fp->nrunning;
+
+- err = curl_easy_pause(temp_fp.easy, CURLPAUSE_CONT);
+- if (err != CURLE_OK) {
+- save_errno = easy_errno(temp_fp.easy, err);
+- goto error_remove;
+- }
+-
+ while (! temp_fp.paused && ! temp_fp.finished)
+ if (wait_perform(&temp_fp) < 0) {
+ save_errno = errno;
+@@ -1084,8 +1090,10 @@ static int libcurl_close(hFILE *fpv)
+ fp->buffer.len = 0;
+ fp->closing = 1;
+ fp->paused = 0;
+- err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
+- if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err);
++ if (! fp->finished) {
++ err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
++ if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err);
++ }
+
+ while (save_errno == 0 && ! fp->paused && ! fp->finished)
+ if (wait_perform(fp) < 0) save_errno = errno;
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