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biology/htslib: Upgrade to 1.10.2

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Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089
This commit is contained in:
Jason W. Bacon 2020-08-03 17:40:04 +00:00
parent 08b4ba2cf0
commit fb3f006dcf
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=544090
12 changed files with 113 additions and 43 deletions
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4
biology/bcftools/Makefile
View File

@ -3,7 +3,7 @@
PORTNAME= bcftools
PORTVERSION= 1.9
PORTREVISION= 1
PORTREVISION= 2
CATEGORIES= biology
MAINTAINER= cartwright@asu.edu
@ -16,8 +16,6 @@ BUILD_DEPENDS= htslib>=1.6:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib
TEST_DEPENDS= bash:shells/bash
CONFLICTS_BUILD=openssl
USES= autoreconf gmake localbase \
perl5 python:env shebangfix

1
biology/cufflinks/Makefile
View File

@ -3,6 +3,7 @@
PORTNAME= cufflinks
DISTVERSIONPREFIX= v
DISTVERSION= 2.2.1-89
PORTREVISION= 1
DISTVERSIONSUFFIX= -gdc3b0cb
CATEGORIES= biology

16
biology/htslib/Makefile
View File

@ -2,28 +2,28 @@
# $FreeBSD$
PORTNAME= htslib
DISTVERSION= 1.9
DISTVERSION= 1.10.2
CATEGORIES= biology devel
MAINTAINER= cartwright@asu.edu
MAINTAINER= jwb@FreeBSD.org
COMMENT= C library for high-throughput sequencing data formats
LICENSE= BSD3CLAUSE MIT
LICENSE_COMB= multi
LICENSE_FILE= ${WRKSRC}/LICENSE
LIB_DEPENDS= libdeflate.so:archivers/libdeflate
TEST_DEPENDS= bash:shells/bash
USES= autoreconf gmake localbase \
pathfix perl5 shebangfix
USES= autoreconf gmake localbase pathfix perl5 shebangfix
USE_GITHUB= yes
GH_ACCOUNT= samtools
USE_PERL5= test
USE_LDCONFIG= yes
GNU_CONFIGURE= yes
GH_ACCOUNT= samtools
GNU_CONFIGURE= yes
PATHFIX_MAKEFILEIN= Makefile
SHEBANG_FILES= test/compare_sam.pl \
test/test.pl
SHEBANG_FILES= test/*.pl
OPTIONS_DEFINE= CURL
OPTIONS_DEFAULT= CURL

6
biology/htslib/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1532906408
SHA256 (samtools-htslib-1.9_GH0.tar.gz) = d2e3cde77b8f874b37453c63390cd992901266336e9f70e871ef42402510467f
SIZE (samtools-htslib-1.9_GH0.tar.gz) = 1285580
TIMESTAMP = 1595116892
SHA256 (samtools-htslib-1.10.2_GH0.tar.gz) = b352eabed6392869dbdea0fe6db10a736a226d1f90036a724a49798f7e81cab7
SIZE (samtools-htslib-1.10.2_GH0.tar.gz) = 1452177

54
biology/htslib/files/patch-Makefile
View File

@ -1,46 +1,52 @@
--- Makefile.orig 2017-10-18 08:03:33 UTC
--- Makefile.orig 2020-08-02 22:52:13 UTC
+++ Makefile
@@ -22,41 +22,26 @@
@@ -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
-
-# Default libraries to link if configure is not used
-htslib_default_libs = -lz -lm -lbz2 -llzma
-
+CC ?= gcc
+AR ?= ar
+RANLIB ?= ranlib
# Default libraries to link if configure is not used
htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl
-CPPFLAGS =
-# 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 -D__FUNCTION__=__func__
-CFLAGS = -g -Wall -O2
+# 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 =
-LIBS = $(htslib_default_libs)
-LDFLAGS = -fvisibility=hidden
+LDFLAGS ?= -fvisibility=hidden
LIBS = $(htslib_default_libs)
-prefix = /usr/local
+prefix = ${PREFIX}
+PREFIX ?= /usr/local
+prefix = $(PREFIX)
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
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
@@ -53,13 +54,13 @@ man5dir = $(mandir)/man5
man7dir = $(mandir)/man7
pkgconfigdir= $(prefix)/libdata/pkgconfig
MKDIR_P = mkdir -p
-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)
+# Use ports BSD_INSTALL_PROGRAM to strip if WITH_DEBUG is not set
+MKDIR_P = mkdir -p
+INSTALL_DATA = ${BSD_INSTALL_DATA}
+INSTALL_DIR = $(MKDIR_P)
+INSTALL_LIB = ${BSD_INSTALL_LIB}
@ -49,9 +55,9 @@
# Set by config.mk if plugins are enabled
plugindir =
@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \
test/thrash_threads5 \
test/thrash_threads6
@@ -98,7 +99,7 @@ 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

65
biology/htslib/files/patch-hfile__libcurl.c
View File

@ -1,6 +1,6 @@
--- hfile_libcurl.c.orig 2017-09-28 11:20:23 UTC
--- hfile_libcurl.c.orig 2019-12-19 09:54:30 UTC
+++ hfile_libcurl.c
@@ -49,6 +49,10 @@ typedef struct {
@@ -74,6 +74,10 @@ typedef struct {
unsigned int size;
} hdrlist;
@ -11,3 +11,64 @@
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;
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, 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;

3
biology/htslib/pkg-plist
View File

@ -30,7 +30,7 @@ include/htslib/vcfutils.h
lib/libhts.a
lib/libhts.so
lib/libhts.so.%%PORTVERSION%%
lib/libhts.so.2
lib/libhts.so.3
libdata/pkgconfig/htslib.pc
man/man1/bgzip.1.gz
man/man1/htsfile.1.gz
@ -38,3 +38,4 @@ man/man1/tabix.1.gz
man/man5/faidx.5.gz
man/man5/sam.5.gz
man/man5/vcf.5.gz
man/man7/htslib-s3-plugin.7.gz

2
biology/jellyfish/Makefile
View File

@ -3,7 +3,7 @@
PORTNAME= Jellyfish
DISTVERSIONPREFIX= v
DISTVERSION= 2.2.10
PORTREVISION= 8
PORTREVISION= 9
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org

2
biology/pbbam/Makefile
View File

@ -2,7 +2,7 @@
PORTNAME= pbbam
DISTVERSION= 0.18.0 # Test with biology/unanimity before upgrading!
PORTREVISION= 4
PORTREVISION= 5
CATEGORIES= biology
# As of March 2018, unanimity is no longer open source.

1
biology/samtools/Makefile
View File

@ -3,6 +3,7 @@
PORTNAME= samtools
DISTVERSION= 1.9
PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= cartwright@asu.edu

1
biology/tabixpp/Makefile
View File

@ -3,6 +3,7 @@
PORTNAME= tabixpp
DISTVERSIONPREFIX= v
DISTVERSION= 1.0.0-10
PORTREVISION= 1
DISTVERSIONSUFFIX= -g6bbe690
CATEGORIES= biology

1
biology/vcflib/Makefile
View File

@ -3,6 +3,7 @@
PORTNAME= vcflib
DISTVERSIONPREFIX= v
DISTVERSION= 1.0.0-rc1-130
PORTREVISION= 1
DISTVERSIONSUFFIX= -g7e3d806
CATEGORIES= biology