Date: Mon, 3 Aug 2020 17:40:04 +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: r544090 - in head/biology: bcftools cufflinks htslib htslib/files jellyfish pbbam samtools tabixpp vcflib Message-ID: <202008031740.073He4iN034001@repo.freebsd.org>
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Author: jwb Date: Mon Aug 3 17:40:04 2020 New Revision: 544090 URL: https://svnweb.freebsd.org/changeset/ports/544090 Log: biology/htslib: Upgrade to 1.10.2 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 Modified: head/biology/bcftools/Makefile head/biology/cufflinks/Makefile head/biology/htslib/Makefile head/biology/htslib/distinfo (contents, props changed) head/biology/htslib/files/patch-Makefile head/biology/htslib/files/patch-hfile__libcurl.c head/biology/htslib/pkg-plist (contents, props changed) head/biology/jellyfish/Makefile head/biology/pbbam/Makefile head/biology/samtools/Makefile head/biology/tabixpp/Makefile head/biology/vcflib/Makefile Modified: head/biology/bcftools/Makefile ============================================================================== --- head/biology/bcftools/Makefile Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/bcftools/Makefile Mon Aug 3 17:40:04 2020 (r544090) @@ -3,7 +3,7 @@ PORTNAME= bcftools PORTVERSION= 1.9 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= cartwright@asu.edu @@ -15,8 +15,6 @@ LICENSE_FILE= ${WRKSRC}/LICENSE 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 Modified: head/biology/cufflinks/Makefile ============================================================================== --- head/biology/cufflinks/Makefile Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/cufflinks/Makefile Mon Aug 3 17:40:04 2020 (r544090) @@ -3,6 +3,7 @@ PORTNAME= cufflinks DISTVERSIONPREFIX= v DISTVERSION= 2.2.1-89 +PORTREVISION= 1 DISTVERSIONSUFFIX= -gdc3b0cb CATEGORIES= biology Modified: head/biology/htslib/Makefile ============================================================================== --- head/biology/htslib/Makefile Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/htslib/Makefile Mon Aug 3 17:40:04 2020 (r544090) @@ -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 Modified: head/biology/htslib/distinfo ============================================================================== --- head/biology/htslib/distinfo Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/htslib/distinfo Mon Aug 3 17:40:04 2020 (r544090) @@ -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 Modified: head/biology/htslib/files/patch-Makefile ============================================================================== --- head/biology/htslib/files/patch-Makefile Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/htslib/files/patch-Makefile Mon Aug 3 17:40:04 2020 (r544090) @@ -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 Modified: head/biology/htslib/files/patch-hfile__libcurl.c ============================================================================== --- head/biology/htslib/files/patch-hfile__libcurl.c Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/htslib/files/patch-hfile__libcurl.c Mon Aug 3 17:40:04 2020 (r544090) @@ -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; Modified: head/biology/htslib/pkg-plist ============================================================================== --- head/biology/htslib/pkg-plist Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/htslib/pkg-plist Mon Aug 3 17:40:04 2020 (r544090) @@ -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 Modified: head/biology/jellyfish/Makefile ============================================================================== --- head/biology/jellyfish/Makefile Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/jellyfish/Makefile Mon Aug 3 17:40:04 2020 (r544090) @@ -3,7 +3,7 @@ PORTNAME= Jellyfish DISTVERSIONPREFIX= v DISTVERSION= 2.2.10 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org Modified: head/biology/pbbam/Makefile ============================================================================== --- head/biology/pbbam/Makefile Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/pbbam/Makefile Mon Aug 3 17:40:04 2020 (r544090) @@ -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. Modified: head/biology/samtools/Makefile ============================================================================== --- head/biology/samtools/Makefile Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/samtools/Makefile Mon Aug 3 17:40:04 2020 (r544090) @@ -3,6 +3,7 @@ PORTNAME= samtools DISTVERSION= 1.9 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= cartwright@asu.edu Modified: head/biology/tabixpp/Makefile ============================================================================== --- head/biology/tabixpp/Makefile Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/tabixpp/Makefile Mon Aug 3 17:40:04 2020 (r544090) @@ -3,6 +3,7 @@ PORTNAME= tabixpp DISTVERSIONPREFIX= v DISTVERSION= 1.0.0-10 +PORTREVISION= 1 DISTVERSIONSUFFIX= -g6bbe690 CATEGORIES= biology Modified: head/biology/vcflib/Makefile ============================================================================== --- head/biology/vcflib/Makefile Mon Aug 3 17:33:40 2020 (r544089) +++ head/biology/vcflib/Makefile Mon Aug 3 17:40:04 2020 (r544090) @@ -3,6 +3,7 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v DISTVERSION= 1.0.0-rc1-130 +PORTREVISION= 1 DISTVERSIONSUFFIX= -g7e3d806 CATEGORIES= biology
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