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Revert "htslib: remove, used for updating biology/htslib"
Module Name: pkgsrc-wip
Committed By: Thomas Klausner <tk%giga.or.at@localhost>
Pushed By: wiz
Date: Sat Jul 25 09:46:13 2020 +0200
Changeset: 2aa119c2112ce794c385a610effa3b68e9c249a9
Modified Files:
Makefile
Added Files:
htslib/DESCR
htslib/Makefile
htslib/PLIST
htslib/buildlink3.mk
htslib/distinfo
htslib/patches/patch-Makefile
htslib/patches/patch-cram_open__trace__file.c
htslib/patches/patch-hfile__libcurl.c
Log Message:
Revert "htslib: remove, used for updating biology/htslib"
This reverts commit 1955414241d219682c08b5c6a2ea665dcf92ac5c.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2aa119c2112ce794c385a610effa3b68e9c249a9
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 3 --
htslib/DESCR | 3 ++
htslib/Makefile | 33 ++++++++++++
htslib/PLIST | 42 +++++++++++++++
htslib/buildlink3.mk | 14 +++++
htslib/distinfo | 9 ++++
htslib/patches/patch-Makefile | 76 ++++++++++++++++++++++++++
htslib/patches/patch-cram_open__trace__file.c | 18 +++++++
htslib/patches/patch-hfile__libcurl.c | 78 +++++++++++++++++++++++++++
9 files changed, 273 insertions(+), 3 deletions(-)
diffs:
diff --git a/Makefile b/Makefile
index 0fd9e4f19e..bfdfb7d1ce 100644
--- a/Makefile
+++ b/Makefile
@@ -2886,7 +2886,6 @@ SUBDIR+= pear-phpcpd
SUBDIR+= pear-phpdcd
SUBDIR+= pear-phploc
SUBDIR+= peercoin
-SUBDIR+= pegtl
SUBDIR+= pentagram
SUBDIR+= petsc
SUBDIR+= pev
@@ -4259,7 +4258,6 @@ SUBDIR+= rdsn-git
SUBDIR+= rdup
SUBDIR+= re2-git
SUBDIR+= readseq
-SUBDIR+= realm-core
SUBDIR+= realpath
SUBDIR+= realtimebattle
SUBDIR+= realvnc
@@ -4786,7 +4784,6 @@ SUBDIR+= tpl
SUBDIR+= tpp
SUBDIR+= tqsllib
SUBDIR+= tr2latex
-SUBDIR+= trac
SUBDIR+= trac-plugins-AuthOpenId
SUBDIR+= trac-plugins-FullBlog
SUBDIR+= trac-plugins-FullBlogNotification
diff --git a/htslib/DESCR b/htslib/DESCR
new file mode 100644
index 0000000000..050ad06ba9
--- /dev/null
+++ b/htslib/DESCR
@@ -0,0 +1,3 @@
+HTSlib is an implementation of a unified C library for accessing common file
+formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
+data. It is the core library used by samtools and bcftools.
diff --git a/htslib/Makefile b/htslib/Makefile
new file mode 100644
index 0000000000..ff598c69be
--- /dev/null
+++ b/htslib/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD$
+
+DISTNAME= htslib-1.10.2
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/}
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= https://www.htslib.org/
+COMMENT= C library for high-throughput sequencing data formats
+LICENSE= mit
+
+USE_TOOLS+= autoconf automake autoreconf bash gmake perl
+GNU_CONFIGURE= yes
+
+SUBST_CLASSES+= version
+SUBST_STAGE.version= pre-configure
+SUBST_SED.version= -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version= configure.ac
+
+REPLACE_PERL+= test/*.pl
+
+CONFIGURE_ARGS+= --enable-libcurl
+PKGCONFIG_OVERRIDE= htslib.pc.in
+TEST_TARGET= test
+
+pre-configure:
+ cd ${WRKSRC} && autoreconf -if
+
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../www/curl/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/htslib/PLIST b/htslib/PLIST
new file mode 100644
index 0000000000..94636d827e
--- /dev/null
+++ b/htslib/PLIST
@@ -0,0 +1,42 @@
+@comment $NetBSD$
+bin/bgzip
+bin/htsfile
+bin/tabix
+include/htslib/bgzf.h
+include/htslib/cram.h
+include/htslib/faidx.h
+include/htslib/hfile.h
+include/htslib/hts.h
+include/htslib/hts_defs.h
+include/htslib/hts_endian.h
+include/htslib/hts_log.h
+include/htslib/hts_os.h
+include/htslib/kbitset.h
+include/htslib/kfunc.h
+include/htslib/khash.h
+include/htslib/khash_str2int.h
+include/htslib/klist.h
+include/htslib/knetfile.h
+include/htslib/kseq.h
+include/htslib/ksort.h
+include/htslib/kstring.h
+include/htslib/regidx.h
+include/htslib/sam.h
+include/htslib/synced_bcf_reader.h
+include/htslib/tbx.h
+include/htslib/thread_pool.h
+include/htslib/vcf.h
+include/htslib/vcf_sweep.h
+include/htslib/vcfutils.h
+lib/libhts.a
+lib/libhts.so
+lib/libhts.so.${PKGVERSION}
+lib/libhts.so.3
+lib/pkgconfig/htslib.pc
+man/man1/bgzip.1
+man/man1/htsfile.1
+man/man1/tabix.1
+man/man5/faidx.5
+man/man5/sam.5
+man/man5/vcf.5
+man/man7/htslib-s3-plugin.7
diff --git a/htslib/buildlink3.mk b/htslib/buildlink3.mk
new file mode 100644
index 0000000000..ac18811a1e
--- /dev/null
+++ b/htslib/buildlink3.mk
@@ -0,0 +1,14 @@
+# $NetBSD$
+
+BUILDLINK_TREE+= htslib
+
+.if !defined(HTSLIB_BUILDLINK3_MK)
+HTSLIB_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.htslib+= htslib>=1.8
+BUILDLINK_ABI_DEPENDS.htslib+= htslib>=1.10.2
+BUILDLINK_PKGSRCDIR.htslib?= ../../wip/htslib
+
+.endif # HTSLIB_BUILDLINK3_MK
+
+BUILDLINK_TREE+= -htslib
diff --git a/htslib/distinfo b/htslib/distinfo
new file mode 100644
index 0000000000..723b6cbeb7
--- /dev/null
+++ b/htslib/distinfo
@@ -0,0 +1,9 @@
+$NetBSD$
+
+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 (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
new file mode 100644
index 0000000000..1d09336074
--- /dev/null
+++ b/htslib/patches/patch-Makefile
@@ -0,0 +1,76 @@
+$NetBSD$
+
+# Respect pkgsrc env
+
+--- Makefile.orig 2019-12-19 09:54:30.000000000 +0000
++++ 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= $(libdir)/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}
++INSTALL_MAN = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
+
+ # 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 $(BUILT_PROGRAMS) plugins
+
+ HTSPREFIX =
+ include htslib_vars.mk
diff --git a/htslib/patches/patch-cram_open__trace__file.c b/htslib/patches/patch-cram_open__trace__file.c
new file mode 100644
index 0000000000..9e4a633a42
--- /dev/null
+++ b/htslib/patches/patch-cram_open__trace__file.c
@@ -0,0 +1,18 @@
+$NetBSD$
+
+# Enhance error message
+
+--- cram/open_trace_file.c.orig 2019-12-19 09:54:30.000000000 +0000
++++ cram/open_trace_file.c
+@@ -204,8 +204,9 @@ mFILE *find_file_url(const char *file, c
+ 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 --git a/htslib/patches/patch-hfile__libcurl.c b/htslib/patches/patch-hfile__libcurl.c
new file mode 100644
index 0000000000..cc6298c065
--- /dev/null
+++ b/htslib/patches/patch-hfile__libcurl.c
@@ -0,0 +1,78 @@
+$NetBSD$
+
+# 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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