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htslib: removed, moved to base
Module Name: pkgsrc-wip
Committed By: Adam Ciarciński <aciarcinski%teonite.com@localhost>
Pushed By: adam
Date: Fri Jul 24 11:23:37 2020 +0200
Changeset: 8cbf7fe790cb866bfd79a54cdff0f75cbd35b09a
Modified Files:
Makefile
pbbam/Makefile
pbbam/buildlink3.mk
tabixpp/Makefile
trinity/Makefile
unanimity/Makefile
vcflib/Makefile
Removed 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:
htslib: removed, moved to base
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8cbf7fe790cb866bfd79a54cdff0f75cbd35b09a
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 -
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 ---------------------------
pbbam/Makefile | 2 +-
pbbam/buildlink3.mk | 2 +-
tabixpp/Makefile | 2 +-
trinity/Makefile | 2 +-
unanimity/Makefile | 2 +-
vcflib/Makefile | 2 +-
15 files changed, 6 insertions(+), 280 deletions(-)
diffs:
diff --git a/Makefile b/Makefile
index 8964d06f27..bfdfb7d1ce 100644
--- a/Makefile
+++ b/Makefile
@@ -1582,7 +1582,6 @@ SUBDIR+= ht2html
SUBDIR+= html-xml-utils
SUBDIR+= html2latex
SUBDIR+= htop-git
-SUBDIR+= htslib
SUBDIR+= httrack
SUBDIR+= hu-go
SUBDIR+= hungrycat
diff --git a/htslib/DESCR b/htslib/DESCR
deleted file mode 100644
index 050ad06ba9..0000000000
--- a/htslib/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-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
deleted file mode 100644
index ff598c69be..0000000000
--- a/htslib/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-# $NetBSD$
-
-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
deleted file mode 100644
index 94636d827e..0000000000
--- a/htslib/PLIST
+++ /dev/null
@@ -1,42 +0,0 @@
-@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
deleted file mode 100644
index ac18811a1e..0000000000
--- a/htslib/buildlink3.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-# $NetBSD$
-
-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
deleted file mode 100644
index 723b6cbeb7..0000000000
--- a/htslib/distinfo
+++ /dev/null
@@ -1,9 +0,0 @@
-$NetBSD$
-
-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
deleted file mode 100644
index 1d09336074..0000000000
--- a/htslib/patches/patch-Makefile
+++ /dev/null
@@ -1,76 +0,0 @@
-$NetBSD$
-
-# 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 $(BUILT_PROGRAMS) plugins
-
- HTSPREFIX =
- include htslib_vars.mk
diff --git a/htslib/patches/patch-cram_open__trace__file.c b/htslib/patches/patch-cram_open__trace__file.c
deleted file mode 100644
index 9e4a633a42..0000000000
--- a/htslib/patches/patch-cram_open__trace__file.c
+++ /dev/null
@@ -1,18 +0,0 @@
-$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
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;
diff --git a/pbbam/Makefile b/pbbam/Makefile
index fcb1092311..4b392278e1 100644
--- a/pbbam/Makefile
+++ b/pbbam/Makefile
@@ -46,7 +46,7 @@ do-install:
cd ${WRKSRC}/include && pax -rw * ${DESTDIR}${PREFIX}/include
.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../wip/htslib/buildlink3.mk"
+.include "../../biology/htslib/buildlink3.mk"
.include "../../security/openssl/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
diff --git a/pbbam/buildlink3.mk b/pbbam/buildlink3.mk
index 5585c9eaaf..b2a64711ef 100644
--- a/pbbam/buildlink3.mk
+++ b/pbbam/buildlink3.mk
@@ -17,7 +17,7 @@ BUILDLINK_PKGSRCDIR.pbbam?= ../../wip/pbbam
# XXX buildlink3 lines below to dependencies, remove them.
# XXX
#.include "../../devel/boost-libs/buildlink3.mk"
-#.include "../../wip/htslib/buildlink3.mk"
+#.include "../../biology/htslib/buildlink3.mk"
#.include "../../security/openssl/buildlink3.mk"
.endif # PBBAM_BUILDLINK3_MK
diff --git a/tabixpp/Makefile b/tabixpp/Makefile
index 7ddbc61083..fcd3dfbc9b 100644
--- a/tabixpp/Makefile
+++ b/tabixpp/Makefile
@@ -30,6 +30,6 @@ pre-configure:
post-install:
cd ${DESTDIR}${PREFIX}/lib && ${LN} -s libtabix.so.1 libtabix.so
-.include "../../wip/htslib/buildlink3.mk"
+.include "../../biology/htslib/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
diff --git a/trinity/Makefile b/trinity/Makefile
index adb10ddfba..1b8a60c040 100644
--- a/trinity/Makefile
+++ b/trinity/Makefile
@@ -149,7 +149,7 @@ do-install:
${DESTDIR}${PREFIX}/libexec/trinity/Trinity
${RM} ${DESTDIR}${PREFIX}/libexec/trinity/util/support_scripts/plugin_install_tests.sh.orig
+.include "../../biology/htslib/buildlink3.mk"
.include "../../lang/python/application.mk"
-.include "../../wip/htslib/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
diff --git a/unanimity/Makefile b/unanimity/Makefile
index 313a953a5a..bc120ae5c3 100644
--- a/unanimity/Makefile
+++ b/unanimity/Makefile
@@ -45,7 +45,7 @@ PORTVERSION= 2016.09.13
.include "../../wip/pbseqan/buildlink3.mk"
.include "../../wip/pbbam/buildlink3.mk"
.include "../../wip/pbcopper/buildlink3.mk"
-.include "../../wip/htslib/buildlink3.mk"
+.include "../../biology/htslib/buildlink3.mk"
.include "../../devel/boost-libs/buildlink3.mk"
.include "../../security/openssl/buildlink3.mk"
.include "../../lang/python/application.mk"
diff --git a/vcflib/Makefile b/vcflib/Makefile
index 0f8a355f5a..c70c48f183 100644
--- a/vcflib/Makefile
+++ b/vcflib/Makefile
@@ -44,7 +44,7 @@ pre-configure:
post-install:
cd ${DESTDIR}${PREFIX}/lib && ${LN} -s libvcflib.so.1 libvcflib.so
-.include "../../wip/htslib/buildlink3.mk"
+.include "../../biology/htslib/buildlink3.mk"
.include "../../wip/tabixpp/buildlink3.mk"
.include "../../wip/smithwaterman/buildlink3.mk"
.include "../../wip/fastahack/buildlink3.mk"
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