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htslib: removed, moved to base

This commit is contained in:
Adam Ciarciński 2020-07-24 11:23:37 +02:00
parent 319045880b
commit 8cbf7fe790
15 changed files with 6 additions and 280 deletions
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1
Makefile
View File

@ -1582,7 +1582,6 @@ SUBDIR+= ht2html
SUBDIR+= html-xml-utils
SUBDIR+= html2latex
SUBDIR+= htop-git
SUBDIR+= htslib
SUBDIR+= httrack
SUBDIR+= hu-go
SUBDIR+= hungrycat

3
htslib/DESCR
View File

@ -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.

33
htslib/Makefile
View File

@ -1,33 +0,0 @@
# $NetBSD$
DISTNAME= htslib-1.10.2
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/}
MAINTAINER= bacon@NetBSD.org
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"

42
htslib/PLIST
View File

@ -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

14
htslib/buildlink3.mk
View File

@ -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

9
htslib/distinfo
View File

@ -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

76
htslib/patches/patch-Makefile
View File

@ -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

18
htslib/patches/patch-cram_open__trace__file.c
View File

@ -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;
}

78
htslib/patches/patch-hfile__libcurl.c
View File

@ -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;

2
pbbam/Makefile
View File

@ -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"

2
pbbam/buildlink3.mk
View File

@ -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

2
tabixpp/Makefile
View File

@ -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"

2
trinity/Makefile
View File

@ -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"

2
unanimity/Makefile
View File

@ -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"

2
vcflib/Makefile
View File

@ -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"