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Date:      Thu, 5 Nov 2020 20:30:50 +0000 (UTC)
From:      "Jason W. Bacon" <jwb@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r554155 - in head/biology/htslib: . files
Message-ID:  <202011052030.0A5KUow4034243@repo.freebsd.org>

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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@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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