Attachment #216561 for bug #248089

View | Details | Raw Unified | Return to bug 248089
Collapse All | Expand All




# $FreeBSD: head/biology/htslib/Makefile 476245 2018-08-02 19:27:13Z fernape $

PORTNAME=	htslib
DISTVERSION=	1.10.2
CATEGORIES=	biology devel

MAINTAINER=	cartwright@asu.edu

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
		pathfix perl5 shebangfix
USE_GITHUB=	yes
GH_ACCOUNT=	samtools
USE_PERL5=	test
USE_LDCONFIG=	yes

GH_ACCOUNT=		samtools
GNU_CONFIGURE=		yes
PATHFIX_MAKEFILEIN=	Makefile
SHEBANG_FILES=		test/*.pl
			test/test.pl

OPTIONS_DEFINE=		CURL
OPTIONS_DEFAULT=	CURL

Lines 1-3 Link Here

(-)/usr/ports/wip/htslib/distinfo (-3 / +3 lines)
1	TIMESTAMP = 1532906408	1	TIMESTAMP = 1595116892
2	SHA256 (samtools-htslib-1.9_GH0.tar.gz) = d2e3cde77b8f874b37453c63390cd992901266336e9f70e871ef42402510467f	2	SHA256 (samtools-htslib-1.10.2_GH0.tar.gz) = b352eabed6392869dbdea0fe6db10a736a226d1f90036a724a49798f7e81cab7
3	SIZE (samtools-htslib-1.9_GH0.tar.gz) = 1285580	3	SIZE (samtools-htslib-1.10.2_GH0.tar.gz) = 1452177




--- Makefile.orig	2020-07-18 23:47:35 UTC
+++ Makefile
@@ -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
+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
 LIBS     = $(htslib_default_libs)
 
-prefix      = /usr/local
-exec_prefix = $(prefix)
+PREFIX      ?= /usr/local
+exec_prefix = $(PREFIX)
 bindir      = $(exec_prefix)/bin
-includedir  = $(prefix)/include
+includedir  = $(PREFIX)/include
 libdir      = $(exec_prefix)/lib
 libexecdir  = $(exec_prefix)/libexec
-datarootdir = $(prefix)/share
+datarootdir = $(PREFIX)/share
 mandir      = $(datarootdir)/man
 man1dir     = $(mandir)/man1
 man5dir     = $(mandir)/man5
 man7dir     = $(mandir)/man7
-pkgconfigdir= $(prefix)/libdata/pkgconfig
+pkgconfigdir= $(PREFIX)/libdata/pkgconfig
 
-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}

 
 # Set by config.mk if plugins are enabled
 plugindir =
@@ -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




--- 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;
     }
 




--- hfile_libcurl.c.orig	2020-07-08 12:52:24 UTC
+++ hfile_libcurl.c
@@ -74,6 +74,10 @@ typedef struct {
     unsigned int size;
 } hdrlist;
 

 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;

Lines 30-36 Link Here

(-)/usr/ports/wip/htslib/pkg-plist (-1 / +2 lines)
30	lib/libhts.a	30	lib/libhts.a
31	lib/libhts.so	31	lib/libhts.so
32	lib/libhts.so.%%PORTVERSION%%	32	lib/libhts.so.%%PORTVERSION%%
33	lib/libhts.so.2	33	lib/libhts.so.3
34	libdata/pkgconfig/htslib.pc	34	libdata/pkgconfig/htslib.pc
35	man/man1/bgzip.1.gz	35	man/man1/bgzip.1.gz
36	man/man1/htsfile.1.gz	36	man/man1/htsfile.1.gz
Lines 38-40 Link Here
38	man/man5/faidx.5.gz	38	man/man5/faidx.5.gz
39	man/man5/sam.5.gz	39	man/man5/sam.5.gz
40	man/man5/vcf.5.gz	40	man/man5/vcf.5.gz
		41	man/man7/htslib-s3-plugin.7.gz

Return to bug 248089

Lines 2-8 Link Here

(-)/usr/ports/wip/htslib/Makefile (-7 / +7 lines)
2	# $FreeBSD: head/biology/htslib/Makefile 476245 2018-08-02 19:27:13Z fernape $	2	# $FreeBSD: head/biology/htslib/Makefile 476245 2018-08-02 19:27:13Z fernape $
3		3
4	PORTNAME= htslib	4	PORTNAME= htslib
5	DISTVERSION= 1.9	5	DISTVERSION= 1.10.2
6	CATEGORIES= biology devel	6	CATEGORIES= biology devel
7		7
8	MAINTAINER= cartwright@asu.edu	8	MAINTAINER= cartwright@asu.edu
Lines 12-29 Link Here
12	LICENSE_COMB= multi	12	LICENSE_COMB= multi
13	LICENSE_FILE= ${WRKSRC}/LICENSE	13	LICENSE_FILE= ${WRKSRC}/LICENSE
14		14
		15	LIB_DEPENDS= libdeflate.so:archivers/libdeflate
15	TEST_DEPENDS= bash:shells/bash	16	TEST_DEPENDS= bash:shells/bash
16		17
17	USES= autoreconf gmake localbase \	18	USES= autoreconf gmake localbase pathfix perl5 shebangfix
18	pathfix perl5 shebangfix
19	USE_GITHUB= yes	19	USE_GITHUB= yes
20	GH_ACCOUNT= samtools
21	USE_PERL5= test	20	USE_PERL5= test
22	USE_LDCONFIG= yes	21	USE_LDCONFIG= yes
23	GNU_CONFIGURE= yes	22
		23	GH_ACCOUNT= samtools
		24	GNU_CONFIGURE= yes
24	PATHFIX_MAKEFILEIN= Makefile	25	PATHFIX_MAKEFILEIN= Makefile
25	SHEBANG_FILES= test/compare_sam.pl \	26	SHEBANG_FILES= test/*.pl
26	test/test.pl
27		27
28	OPTIONS_DEFINE= CURL	28	OPTIONS_DEFINE= CURL
29	OPTIONS_DEFAULT= CURL	29	OPTIONS_DEFAULT= CURL

Lines 1-46 Link Here

(-)/usr/ports/wip/htslib/files/patch-Makefile (-23 / +36 lines)
1	--- Makefile.orig 2017-10-18 08:03:33 UTC	1	--- Makefile.orig 2020-07-18 23:47:35 UTC
2	+++ Makefile	2	+++ Makefile
3	@@ -22,41 +22,26 @@	3	@@ -22,44 +22,43 @@
4	# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER	4	# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
5	# DEALINGS IN THE SOFTWARE.	5	# DEALINGS IN THE SOFTWARE.
6		6
7	-CC = gcc	7	-CC = gcc
8	-AR = ar	8	-AR = ar
9	-RANLIB = ranlib	9	-RANLIB = ranlib
10	-	10	+CC ?= gcc
11	-# Default libraries to link if configure is not used	11	+AR ?= ar
12	-htslib_default_libs = -lz -lm -lbz2 -llzma	12	+RANLIB ?= ranlib
13	-	13
		14	# Default libraries to link if configure is not used
		15	htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl
		16
14	-CPPFLAGS =	17	-CPPFLAGS =
15	-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat	18	+# CPPFLAGS =
16	-# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600	19	# TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64
17	-#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__	20	# to CFLAGS manually, here or in config.mk if the latter exists.
18	-CFLAGS = -g -Wall -O2	21	# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
		22	# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
		23	#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
		24	-CFLAGS = -g -Wall -O2 -fvisibility=hidden
		25	+CFLAGS ?= -g -Wall -O2 -fvisibility=hidden
19	EXTRA_CFLAGS_PIC = -fpic	26	EXTRA_CFLAGS_PIC = -fpic
20	-LDFLAGS =	27	-LDFLAGS = -fvisibility=hidden
21	-LIBS = $(htslib_default_libs)	28	+LDFLAGS ?= -fvisibility=hidden
		29	LIBS = $(htslib_default_libs)
22		30
23	-prefix = /usr/local	31	-prefix = /usr/local
24	+prefix = ${PREFIX}	32	-exec_prefix = $(prefix)
25	exec_prefix = $(prefix)	33	+PREFIX ?= /usr/local
		34	+exec_prefix = $(PREFIX)
26	bindir = $(exec_prefix)/bin	35	bindir = $(exec_prefix)/bin
27	includedir = $(prefix)/include	36	-includedir = $(prefix)/include
		37	+includedir = $(PREFIX)/include
28	libdir = $(exec_prefix)/lib	38	libdir = $(exec_prefix)/lib
29	libexecdir = $(exec_prefix)/libexec	39	libexecdir = $(exec_prefix)/libexec
30	datarootdir = $(prefix)/share	40	-datarootdir = $(prefix)/share
31	-mandir = $(datarootdir)/man	41	+datarootdir = $(PREFIX)/share
32	+mandir = $(prefix)/man	42	mandir = $(datarootdir)/man
33	man1dir = $(mandir)/man1	43	man1dir = $(mandir)/man1
34	man5dir = $(mandir)/man5	44	man5dir = $(mandir)/man5
35	pkgconfigdir= $(prefix)/libdata/pkgconfig	45	man7dir = $(mandir)/man7
		46	-pkgconfigdir= $(prefix)/libdata/pkgconfig
		47	+pkgconfigdir= $(PREFIX)/libdata/pkgconfig
36		48
37	MKDIR_P = mkdir -p	49	-MKDIR_P = mkdir -p
38	-INSTALL = install -p	50	-INSTALL = install -p
39	-INSTALL_DATA = $(INSTALL) -m 644	51	-INSTALL_DATA = $(INSTALL) -m 644
40	-INSTALL_DIR = $(MKDIR_P) -m 755	52	-INSTALL_DIR = $(MKDIR_P) -m 755
41	-INSTALL_LIB = $(INSTALL_DATA)	53	-INSTALL_LIB = $(INSTALL_DATA)
42	-INSTALL_MAN = $(INSTALL_DATA)	54	-INSTALL_MAN = $(INSTALL_DATA)
43	-INSTALL_PROGRAM = $(INSTALL)	55	-INSTALL_PROGRAM = $(INSTALL)
		56	+MKDIR_P = mkdir -p
44	+INSTALL_DATA = ${BSD_INSTALL_DATA}	57	+INSTALL_DATA = ${BSD_INSTALL_DATA}
45	+INSTALL_DIR = $(MKDIR_P)	58	+INSTALL_DIR = $(MKDIR_P)
46	+INSTALL_LIB = ${BSD_INSTALL_LIB}	59	+INSTALL_LIB = ${BSD_INSTALL_LIB}
Lines 49-57 Link Here
49		62
50	# Set by config.mk if plugins are enabled	63	# Set by config.mk if plugins are enabled
51	plugindir =	64	plugindir =
52	@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \	65	@@ -98,7 +97,7 @@ BUILT_THRASH_PROGRAMS = \
53	test/thrash_threads5 \	66	test/thrash_threads6 \
54	test/thrash_threads6	67	test/thrash_threads7
55		68
56	-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)	69	-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
57	+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins	70	+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins

Line 0 Link Here

(-)/usr/ports/wip/htslib/files/patch-cram_open__trace__file.c (+14 lines)
	1	--- cram/open_trace_file.c.orig 2020-07-08 12:52:24 UTC
	2	+++ cram/open_trace_file.c
	3	@@ -205,8 +205,9 @@ mFILE find_file_url(const char file, char *url) {
	4	goto fail;
	5	}
	6	}
	7	- if (hclose(hf) < 0 \|\| len < 0) {
	8	- hts_log_warning("Failed to read reference \"%s\": %s", path, strerror(errno));
	9	+ int close_status = hclose(hf);
	10	+ if (close_status < 0 \|\| len < 0) {
	11	+ hts_log_warning("Failed to read reference \"%s\": %s close_status = %d len = %ld", path, strerror(errno));
	12	goto fail;
	13	}
	14

Lines 1-6 Link Here

(-)/usr/ports/wip/htslib/files/patch-hfile__libcurl.c (-2 / +89 lines)
1	--- hfile_libcurl.c.orig 2017-09-28 11:20:23 UTC	1	--- hfile_libcurl.c.orig 2020-07-08 12:52:24 UTC
2	+++ hfile_libcurl.c	2	+++ hfile_libcurl.c
3	@@ -49,6 +49,10 @@ typedef struct {	3	@@ -74,6 +74,10 @@ typedef struct {
4	unsigned int size;	4	unsigned int size;
5	} hdrlist;	5	} hdrlist;
6		6
Lines 11-13 Link Here
11	typedef struct {	11	typedef struct {
12	hdrlist fixed; // List of headers supplied at hopen()	12	hdrlist fixed; // List of headers supplied at hopen()
13	hdrlist extra; // List of headers from callback	13	hdrlist extra; // List of headers from callback
		14	@@ -126,6 +130,8 @@ static int restart_from_position(hFILE_libcurl *fp, of
		15
		16	static int http_status_errno(int status)
		17	{
		18	+ fprintf(stderr, "http_status_errno: status = %d\n", status);
		19	+
		20	if (status >= 500)
		21	switch (status) {
		22	case 501: return ENOSYS;
		23	@@ -151,6 +157,8 @@ static int easy_errno(CURL *easy, CURLcode err)
		24	{
		25	long lval;
		26
		27	+ fprintf(stderr, "easy_errno: err = %d\n", err);
		28	+
		29	switch (err) {
		30	case CURLE_OK:
		31	return 0;
		32	@@ -221,12 +229,16 @@ static int easy_errno(CURL *easy, CURLcode err)
		33	return EEXIST;
		34
		35	default:
		36	+ hts_log_error("Libcurl reported error %d (%s)", (int) err,
		37	+ curl_easy_strerror(err));
		38	return EIO;
		39	}
		40	}
		41
		42	static int multi_errno(CURLMcode errm)
		43	{
		44	+ fprintf(stderr, "multi_errno: errm = %d\n", errm);
		45	+
		46	switch (errm) {
		47	case CURLM_CALL_MULTI_PERFORM:
		48	case CURLM_OK:
		49	@@ -241,6 +253,8 @@ static int multi_errno(CURLMcode errm)
		50	return ENOMEM;
		51
		52	default:
		53	+ hts_log_error("Libcurl reported error %d (%s)", (int) errm,
		54	+ curl_multi_strerror(errm));
		55	return EIO;
		56	}
		57	}
		58	@@ -818,9 +832,13 @@ static ssize_t libcurl_read(hFILE fpv, void bufferv,
		59	fp->buffer.ptr.rd = buffer;
		60	fp->buffer.len = nbytes;
		61	fp->paused = 0;
		62	- err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
		63	- if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; }
		64	-
		65	+ if (! fp->finished) {
		66	+ err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
		67	+ if (err != CURLE_OK) {
		68	+ errno = easy_errno(fp->easy, err);
		69	+ return -1;
		70	+ }
		71	+ }
		72	while (! fp->paused && ! fp->finished) {
		73	if (wait_perform(fp) < 0) return -1;
		74	}
		75	@@ -1046,12 +1064,6 @@ static int restart_from_position(hFILE_libcurl *fp, of
		76	}
		77	temp_fp.nrunning = ++fp->nrunning;
78
79	- err = curl_easy_pause(temp_fp.easy, CURLPAUSE_CONT);
80	- if (err != CURLE_OK) {
81	- save_errno = easy_errno(temp_fp.easy, err);
82	- goto error_remove;
83	- }
84	-
85	while (! temp_fp.paused && ! temp_fp.finished)
86	if (wait_perform(&temp_fp) < 0) {
87	save_errno = errno;
88	@@ -1127,8 +1139,10 @@ static int libcurl_close(hFILE *fpv)
89	fp->buffer.len = 0;
90	fp->closing = 1;
91	fp->paused = 0;
92	- err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
93	- if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err);
94	+ if (! fp->finished) {
95	+ err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
96	+ if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err);
97	+ }
98
99	while (save_errno == 0 && ! fp->paused && ! fp->finished)
100	if (wait_perform(fp) < 0) save_errno = errno;