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htslib: Upgrade to latest upstream commit
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Mon Jul 27 09:30:34 2020 -0500
Changeset: 127009ca9e927b9cdaebe5a4fd8a11d6dc7fc095
Modified Files:
htslib/Makefile
htslib/PLIST
htslib/distinfo
htslib/patches/patch-Makefile
Removed Files:
htslib/patches/patch-hfile__libcurl.c
Log Message:
htslib: Upgrade to latest upstream commit
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=127009ca9e927b9cdaebe5a4fd8a11d6dc7fc095
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
htslib/Makefile | 3 +-
htslib/PLIST | 3 +-
htslib/distinfo | 11 +++--
htslib/patches/patch-Makefile | 48 +++++++++------------
htslib/patches/patch-hfile__libcurl.c | 78 -----------------------------------
5 files changed, 28 insertions(+), 115 deletions(-)
diffs:
diff --git a/htslib/Makefile b/htslib/Makefile
index ff598c69be..c6f5b28cc1 100644
--- a/htslib/Makefile
+++ b/htslib/Makefile
@@ -1,8 +1,9 @@
# $NetBSD$
-DISTNAME= htslib-1.10.2
+DISTNAME= htslib-1.10.2.110
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/}
+GITHUB_TAG= da595880d134b29fb62f726b72bdc6302ffc9ccc
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://www.htslib.org/
diff --git a/htslib/PLIST b/htslib/PLIST
index 94636d827e..7ee80d6df9 100644
--- a/htslib/PLIST
+++ b/htslib/PLIST
@@ -17,6 +17,7 @@ include/htslib/khash.h
include/htslib/khash_str2int.h
include/htslib/klist.h
include/htslib/knetfile.h
+include/htslib/kroundup.h
include/htslib/kseq.h
include/htslib/ksort.h
include/htslib/kstring.h
@@ -30,7 +31,7 @@ include/htslib/vcf_sweep.h
include/htslib/vcfutils.h
lib/libhts.a
lib/libhts.so
-lib/libhts.so.${PKGVERSION}
+lib/libhts.so.1.10.2
lib/libhts.so.3
lib/pkgconfig/htslib.pc
man/man1/bgzip.1
diff --git a/htslib/distinfo b/htslib/distinfo
index 723b6cbeb7..bd59f3a614 100644
--- a/htslib/distinfo
+++ b/htslib/distinfo
@@ -1,9 +1,8 @@
$NetBSD$
-SHA1 (htslib-1.10.2.tar.gz) = 0ac4b86e49556d7dcaa89d4cce2661c9ca706631
-RMD160 (htslib-1.10.2.tar.gz) = 6d8b6a362297345420dc9acc544029276ce4b1b6
-SHA512 (htslib-1.10.2.tar.gz) = 7a91c15ca1de35653d068dc57ae511ad791ae0bd8504867d4e60c46e813e58b441409541197cde3b2a37840e60331336aebc627ecbf5c64fca1af63dd05f8f9e
-Size (htslib-1.10.2.tar.gz) = 1452177 bytes
-SHA1 (patch-Makefile) = e13333dd97ecd6c6753d14c1b738d6e5934a2911
+SHA1 (htslib-1.10.2.110-da595880d134b29fb62f726b72bdc6302ffc9ccc.tar.gz) = cf698267f2701b71714cfd18754a7108a46c542d
+RMD160 (htslib-1.10.2.110-da595880d134b29fb62f726b72bdc6302ffc9ccc.tar.gz) = ff8c0d69cccd94349082da474ff0288d36d2ed21
+SHA512 (htslib-1.10.2.110-da595880d134b29fb62f726b72bdc6302ffc9ccc.tar.gz) = f3ed4b25521694e9655ad5ad0229e012f281c98be610e6b4d3c71892565a06f365ca14a19493280db4d0f6143111eb5638381cf070a1858b63e30e2ce24a28ae
+Size (htslib-1.10.2.110-da595880d134b29fb62f726b72bdc6302ffc9ccc.tar.gz) = 1477520 bytes
+SHA1 (patch-Makefile) = 571ddd0fad8b0bc8a1f5be9af33e3561aefe784d
SHA1 (patch-cram_open__trace__file.c) = 49b47e13786317e652a8ec810cc91f10d21bb8ea
-SHA1 (patch-hfile__libcurl.c) = 2a143818f1099ef01c57a3c904060a76abb63f14
diff --git a/htslib/patches/patch-Makefile b/htslib/patches/patch-Makefile
index 1d09336074..aa38a042ac 100644
--- a/htslib/patches/patch-Makefile
+++ b/htslib/patches/patch-Makefile
@@ -1,10 +1,10 @@
$NetBSD$
-# Respect pkgsrc env
+# Respect build environment
---- Makefile.orig 2019-12-19 09:54:30.000000000 +0000
+--- Makefile.orig 2020-07-21 09:19:56.000000000 +0000
+++ Makefile
-@@ -22,44 +22,43 @@
+@@ -22,31 +22,31 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
@@ -46,31 +46,21 @@ $NetBSD$
mandir = $(datarootdir)/man
man1dir = $(mandir)/man1
man5dir = $(mandir)/man5
- man7dir = $(mandir)/man7
- pkgconfigdir= $(libdir)/pkgconfig
+@@ -69,7 +69,7 @@ BUILT_PROGRAMS = \
+ htsfile \
+ tabix
--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}
-+INSTALL_MAN = ${BSD_INSTALL_MAN}
-+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
+-BUILT_TEST_PROGRAMS = \
++BUILT_TEST_PROGRAMS ?= \
+ test/hts_endian \
+ test/fieldarith \
+ test/hfile \
+@@ -90,7 +90,7 @@ BUILT_TEST_PROGRAMS = \
+ test/test-bcf-translate \
+ test/test-parse-reg
- # 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 $(BUILT_PROGRAMS) plugins
-
- HTSPREFIX =
- include htslib_vars.mk
+-BUILT_THRASH_PROGRAMS = \
++BUILT_THRASH_PROGRAMS ?= \
+ test/thrash_threads1 \
+ test/thrash_threads2 \
+ test/thrash_threads3 \
diff --git a/htslib/patches/patch-hfile__libcurl.c b/htslib/patches/patch-hfile__libcurl.c
deleted file mode 100644
index cc6298c065..0000000000
--- a/htslib/patches/patch-hfile__libcurl.c
+++ /dev/null
@@ -1,78 +0,0 @@
-$NetBSD$
-
-# recent libcurl compatibility
-
---- hfile_libcurl.c.orig 2019-12-19 09:54:30.000000000 +0000
-+++ hfile_libcurl.c
-@@ -74,6 +74,10 @@ typedef struct {
- unsigned int size;
- } hdrlist;
-
-+#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, CURLco
- 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,
- 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_l
- }
- 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;
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