Attachment 216561 Details for Bug 248089 – Unified diff

[patch] Unified diff

htslib.diff (text/plain), 9.95 KB, created by Jason W. Bacon on 2020-07-19 01:57:03 UTC

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Creator: Jason W. Bacon

Created: 2020-07-19 01:57:03 UTC

Size: 9.95 KB

patch

obsolete

>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/htslib/Makefile /usr/ports/wip/htslib/Makefile
>--- /usr/ports/biology/htslib/Makefile	2019-04-18 07:08:58.314972000 -0500
>+++ /usr/ports/wip/htslib/Makefile	2020-07-18 20:49:50.987417000 -0500
>@@ -2,7 +2,7 @@
> # $FreeBSD: head/biology/htslib/Makefile 476245 2018-08-02 19:27:13Z fernape $
> 
> PORTNAME=	htslib
>-DISTVERSION=	1.9
>+DISTVERSION=	1.10.2
> CATEGORIES=	biology devel
> 
> MAINTAINER=	cartwright@asu.edu
>@@ -12,18 +12,18 @@
> 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
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/htslib/distinfo /usr/ports/wip/htslib/distinfo
>--- /usr/ports/biology/htslib/distinfo	2019-04-18 07:08:58.315223000 -0500
>+++ /usr/ports/wip/htslib/distinfo	2020-07-18 20:48:19.646276000 -0500
>@@ -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
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/htslib/files/patch-Makefile /usr/ports/wip/htslib/files/patch-Makefile
>--- /usr/ports/biology/htslib/files/patch-Makefile	2019-04-18 07:08:58.315453000 -0500
>+++ /usr/ports/wip/htslib/files/patch-Makefile	2020-07-18 20:48:03.074414000 -0500
>@@ -1,46 +1,59 @@
>---- Makefile.orig	2017-10-18 08:03:33 UTC
>+--- Makefile.orig	2020-07-18 23:47:35 UTC
> +++ Makefile
>-@@ -22,41 +22,26 @@
>+@@ -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
>--
>--# 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}
>- exec_prefix = $(prefix)
>+-exec_prefix = $(prefix)
>++PREFIX      ?= /usr/local
>++exec_prefix = $(PREFIX)
>  bindir      = $(exec_prefix)/bin
>- includedir  = $(prefix)/include
>+-includedir  = $(prefix)/include
>++includedir  = $(PREFIX)/include
>  libdir      = $(exec_prefix)/lib
>  libexecdir  = $(exec_prefix)/libexec
>- datarootdir = $(prefix)/share
>--mandir      = $(datarootdir)/man
>-+mandir      = $(prefix)/man
>+-datarootdir = $(prefix)/share
>++datarootdir = $(PREFIX)/share
>+ mandir      = $(datarootdir)/man
>  man1dir     = $(mandir)/man1
>  man5dir     = $(mandir)/man5
>- pkgconfigdir= $(prefix)/libdata/pkgconfig
>+ man7dir     = $(mandir)/man7
>+-pkgconfigdir= $(prefix)/libdata/pkgconfig
>++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)
>++MKDIR_P         = mkdir -p
> +INSTALL_DATA    = ${BSD_INSTALL_DATA}
> +INSTALL_DIR     = $(MKDIR_P)
> +INSTALL_LIB     = ${BSD_INSTALL_LIB}
>@@ -49,9 +62,9 @@
>  
>  # Set by config.mk if plugins are enabled
>  plugindir =
>-@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \
>- 	test/thrash_threads5 \
>- 	test/thrash_threads6
>+@@ -98,7 +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
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/htslib/files/patch-cram_open__trace__file.c /usr/ports/wip/htslib/files/patch-cram_open__trace__file.c
>--- /usr/ports/biology/htslib/files/patch-cram_open__trace__file.c	1969-12-31 18:00:00.000000000 -0600
>+++ /usr/ports/wip/htslib/files/patch-cram_open__trace__file.c	2020-07-14 09:01:07.376319000 -0500
>@@ -0,0 +1,14 @@
>+--- cram/open_trace_file.c.orig	2020-07-08 12:52:24 UTC
>++++ cram/open_trace_file.c
>+@@ -205,8 +205,9 @@ mFILE *find_file_url(const char *file, char *url) {
>+             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;
>+     }
>+ 
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/htslib/files/patch-hfile__libcurl.c /usr/ports/wip/htslib/files/patch-hfile__libcurl.c
>--- /usr/ports/biology/htslib/files/patch-hfile__libcurl.c	2019-04-18 07:08:58.315683000 -0500
>+++ /usr/ports/wip/htslib/files/patch-hfile__libcurl.c	2020-07-14 09:01:07.376509000 -0500
>@@ -1,6 +1,6 @@
>---- hfile_libcurl.c.orig	2017-09-28 11:20:23 UTC
>+--- hfile_libcurl.c.orig	2020-07-08 12:52:24 UTC
> +++ hfile_libcurl.c
>-@@ -49,6 +49,10 @@ typedef struct {
>+@@ -74,6 +74,10 @@ typedef struct {
>      unsigned int size;
>  } hdrlist;
>  
>@@ -11,3 +11,90 @@
>  typedef struct {
>      hdrlist fixed;                   // List of headers supplied at hopen()
>      hdrlist extra;                   // List of headers from callback
>+@@ -126,6 +130,8 @@ static int restart_from_position(hFILE_libcurl *fp, of
>+ 
>+ static int http_status_errno(int status)
>+ {
>++    fprintf(stderr, "http_status_errno: status = %d\n", status);
>++
>+     if (status >= 500)
>+         switch (status) {
>+         case 501: return ENOSYS;
>+@@ -151,6 +157,8 @@ static int easy_errno(CURL *easy, CURLcode err)
>+ {
>+     long lval;
>+ 
>++    fprintf(stderr, "easy_errno: err = %d\n", err);
>++
>+     switch (err) {
>+     case CURLE_OK:
>+         return 0;
>+@@ -221,12 +229,16 @@ 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;
>+     }
>+ }
>+ 
>+ static int multi_errno(CURLMcode errm)
>+ {
>++    fprintf(stderr, "multi_errno: errm = %d\n", errm);
>++
>+     switch (errm) {
>+     case CURLM_CALL_MULTI_PERFORM:
>+     case CURLM_OK:
>+@@ -241,6 +253,8 @@ 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;
>+     }
>+ }
>+@@ -818,9 +832,13 @@ 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;
>+         }
>+@@ -1046,12 +1064,6 @@ 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;
>+@@ -1127,8 +1139,10 @@ 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;
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/htslib/pkg-plist /usr/ports/wip/htslib/pkg-plist
>--- /usr/ports/biology/htslib/pkg-plist	2019-04-18 07:08:58.317173000 -0500
>+++ /usr/ports/wip/htslib/pkg-plist	2020-07-18 20:48:03.076477000 -0500
>@@ -30,7 +30,7 @@
> 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/man5/faidx.5.gz
> man/man5/sam.5.gz
> man/man5/vcf.5.gz
>+man/man7/htslib-s3-plugin.7.gz

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Attachments on bug 248089: 216561