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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 09:45:17 2020 +0200
Changeset:	1955414241d219682c08b5c6a2ea665dcf92ac5c

Modified Files:
	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: remove, used for updating biology/htslib

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1955414241d219682c08b5c6a2ea665dcf92ac5c

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, 3 insertions(+), 273 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index bfdfb7d1ce..0fd9e4f19e 100644
--- a/Makefile
+++ b/Makefile
@@ -2886,6 +2886,7 @@ SUBDIR+=	pear-phpcpd
 SUBDIR+=	pear-phpdcd
 SUBDIR+=	pear-phploc
 SUBDIR+=	peercoin
+SUBDIR+=	pegtl
 SUBDIR+=	pentagram
 SUBDIR+=	petsc
 SUBDIR+=	pev
@@ -4258,6 +4259,7 @@ SUBDIR+=	rdsn-git
 SUBDIR+=	rdup
 SUBDIR+=	re2-git
 SUBDIR+=	readseq
+SUBDIR+=	realm-core
 SUBDIR+=	realpath
 SUBDIR+=	realtimebattle
 SUBDIR+=	realvnc
@@ -4784,6 +4786,7 @@ 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
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;


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