svn commit: r554155 - in head/biology/htslib: . files
Jason W. Bacon
jwb at FreeBSD.org
Thu Nov 5 20:30:52 UTC 2020
Author: jwb
Date: Thu Nov 5 20:30:50 2020
New Revision: 554155
URL: https://svnweb.freebsd.org/changeset/ports/554155
Log:
biology/htslib: Upgrade to 1.11.0
Numerous bug fixes, new features and performance improvements since 1.10
https://github.com/samtools/htslib/releases/tag/1.11
Reported by: portscout
Added:
head/biology/htslib/files/patch-hts.c (contents, props changed)
head/biology/htslib/files/patch-sam.c (contents, props changed)
Modified:
head/biology/htslib/Makefile
head/biology/htslib/distinfo
head/biology/htslib/files/patch-Makefile
head/biology/htslib/files/patch-hfile__libcurl.c
head/biology/htslib/pkg-plist
Modified: head/biology/htslib/Makefile
==============================================================================
--- head/biology/htslib/Makefile Thu Nov 5 19:34:29 2020 (r554154)
+++ head/biology/htslib/Makefile Thu Nov 5 20:30:50 2020 (r554155)
@@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= htslib
-DISTVERSION= 1.10.2
+DISTVERSION= 1.11.0
CATEGORIES= biology devel
MAINTAINER= jwb at FreeBSD.org
Modified: head/biology/htslib/distinfo
==============================================================================
--- head/biology/htslib/distinfo Thu Nov 5 19:34:29 2020 (r554154)
+++ head/biology/htslib/distinfo Thu Nov 5 20:30:50 2020 (r554155)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1595116892
-SHA256 (samtools-htslib-1.10.2_GH0.tar.gz) = b352eabed6392869dbdea0fe6db10a736a226d1f90036a724a49798f7e81cab7
-SIZE (samtools-htslib-1.10.2_GH0.tar.gz) = 1452177
+TIMESTAMP = 1602982298
+SHA256 (samtools-htslib-1.11.0_GH0.tar.gz) = 55356e78f25a20194488d94308335f409c3757101398961388caf38d3cce12dd
+SIZE (samtools-htslib-1.11.0_GH0.tar.gz) = 1485848
Modified: head/biology/htslib/files/patch-Makefile
==============================================================================
--- head/biology/htslib/files/patch-Makefile Thu Nov 5 19:34:29 2020 (r554154)
+++ head/biology/htslib/files/patch-Makefile Thu Nov 5 20:30:50 2020 (r554155)
@@ -1,31 +1,7 @@
---- Makefile.orig 2020-08-02 22:52:13 UTC
+--- Makefile.orig 2020-10-18 00:44:56 UTC
+++ Makefile
-@@ -22,25 +22,26 @@
- # 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
+@@ -40,7 +40,8 @@ EXTRA_CFLAGS_PIC = -fpic
+ LDFLAGS = -fvisibility=hidden
LIBS = $(htslib_default_libs)
-prefix = /usr/local
@@ -34,7 +10,7 @@
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
includedir = $(prefix)/include
-@@ -53,13 +54,13 @@ man5dir = $(mandir)/man5
+@@ -53,13 +54,14 @@ man5dir = $(mandir)/man5
man7dir = $(mandir)/man7
pkgconfigdir= $(prefix)/libdata/pkgconfig
@@ -47,6 +23,7 @@
-INSTALL_PROGRAM = $(INSTALL)
+# Use ports BSD_INSTALL_PROGRAM to strip if WITH_DEBUG is not set
+MKDIR_P = mkdir -p
++INSTALL = install -p
+INSTALL_DATA = ${BSD_INSTALL_DATA}
+INSTALL_DIR = $(MKDIR_P)
+INSTALL_LIB = ${BSD_INSTALL_LIB}
@@ -55,12 +32,12 @@
# Set by config.mk if plugins are enabled
plugindir =
-@@ -98,7 +99,7 @@ BUILT_THRASH_PROGRAMS = \
+@@ -100,7 +102,7 @@ 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
+-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) \
++all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \
+ htslib_static.mk htslib-uninstalled.pc
HTSPREFIX =
- include htslib_vars.mk
Modified: head/biology/htslib/files/patch-hfile__libcurl.c
==============================================================================
--- head/biology/htslib/files/patch-hfile__libcurl.c Thu Nov 5 19:34:29 2020 (r554154)
+++ head/biology/htslib/files/patch-hfile__libcurl.c Thu Nov 5 20:30:50 2020 (r554155)
@@ -1,74 +1,24 @@
---- hfile_libcurl.c.orig 2019-12-19 09:54:30 UTC
+--- hfile_libcurl.c.orig 2020-09-22 12:15:49 UTC
+++ hfile_libcurl.c
-@@ -74,6 +74,10 @@ typedef struct {
- unsigned int size;
- } hdrlist;
+@@ -22,6 +22,10 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR O
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE. */
+#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, CURLcode err)
- return EEXIST;
+ #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
+ #include <config.h>
- 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;
+@@ -73,6 +77,10 @@ typedef struct {
+ unsigned int num;
+ unsigned int size;
+ } hdrlist;
++
++#ifndef ENOTRECOVERABLE
++#define ENOTRECOVERABLE EIO
++#endif
- 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, void *bufferv,
- 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_libcurl *fp, of
- }
- 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;
+ typedef struct {
+ hdrlist fixed; // List of headers supplied at hopen()
Added: head/biology/htslib/files/patch-hts.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/htslib/files/patch-hts.c Thu Nov 5 20:30:50 2020 (r554155)
@@ -0,0 +1,10 @@
+--- hts.c.orig 2020-10-18 00:49:42 UTC
++++ hts.c
+@@ -39,6 +39,7 @@ DEALINGS IN THE SOFTWARE. */
+ #include <time.h>
+ #include <sys/stat.h>
+ #include <assert.h>
++#include <unistd.h> // R_OK
+
+ #include "htslib/hts.h"
+ #include "htslib/bgzf.h"
Added: head/biology/htslib/files/patch-sam.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/htslib/files/patch-sam.c Thu Nov 5 20:30:50 2020 (r554155)
@@ -0,0 +1,10 @@
+--- sam.c.orig 2020-10-18 00:50:46 UTC
++++ sam.c
+@@ -35,6 +35,7 @@ DEALINGS IN THE SOFTWARE. */
+ #include <assert.h>
+ #include <signal.h>
+ #include <inttypes.h>
++#include <unistd.h> // usleep()
+
+ // Suppress deprecation message for cigar_tab, which we initialise
+ #include "htslib/hts_defs.h"
Modified: head/biology/htslib/pkg-plist
==============================================================================
--- head/biology/htslib/pkg-plist Thu Nov 5 19:34:29 2020 (r554154)
+++ head/biology/htslib/pkg-plist Thu Nov 5 20:30:50 2020 (r554155)
@@ -16,6 +16,7 @@ include/htslib/khash.h
include/htslib/khash_str2int.h
include/htslib/klist.h
include/htslib/knetfile.h
+include/htslib/kroundup.h
include/htslib/kseq.h
include/htslib/ksort.h
include/htslib/kstring.h
@@ -29,7 +30,7 @@ include/htslib/vcf_sweep.h
include/htslib/vcfutils.h
lib/libhts.a
lib/libhts.so
-lib/libhts.so.%%PORTVERSION%%
+lib/libhts.so.1.11
lib/libhts.so.3
libdata/pkgconfig/htslib.pc
man/man1/bgzip.1.gz
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