svn commit: r562501 - in head/biology/bedtools: . files
Jason W. Bacon
jwb at FreeBSD.org
Sun Jan 24 18:25:40 UTC 2021
Author: jwb
Date: Sun Jan 24 18:25:39 2021
New Revision: 562501
URL: https://svnweb.freebsd.org/changeset/ports/562501
Log:
biology/bedtools: Upgrade to 2.30.0
Several bug fixes and performance enhancements
Reported by: portscout
Added:
head/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp (contents, props changed)
Deleted:
head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h
Modified:
head/biology/bedtools/Makefile
head/biology/bedtools/distinfo
head/biology/bedtools/files/patch-Makefile
head/biology/bedtools/files/patch-src_utils_htslib_Makefile
Modified: head/biology/bedtools/Makefile
==============================================================================
--- head/biology/bedtools/Makefile Sun Jan 24 18:15:20 2021 (r562500)
+++ head/biology/bedtools/Makefile Sun Jan 24 18:25:39 2021 (r562501)
@@ -2,7 +2,7 @@
PORTNAME= bedtools
DISTVERSIONPREFIX= v
-DISTVERSION= 2.29.2
+DISTVERSION= 2.30.0
CATEGORIES= biology
MAINTAINER= jwb at FreeBSD.org
@@ -15,20 +15,12 @@ TEST_DEPENDS= bash:shells/bash
USES= compiler:c++11-lang gmake python
USE_GITHUB= yes
+
GH_ACCOUNT= arq5x
GH_PROJECT= bedtools2
-post-extract:
-# Avoid conflict with C++20 <version> by adding .txt suffix
- @${MV} ${WRKSRC}/src/utils/gzstream/version \
- ${WRKSRC}/src/utils/gzstream/version.txt
-
pre-configure:
@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile
- @${REINPLACE_CMD} -e 's|@\$$(CXX)|$$(CXX)|g' \
- ${WRKSRC}/*/Makefile \
- ${WRKSRC}/*/*/Makefile \
- ${WRKSRC}/*/*/*/Makefile
post-install:
${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools
Modified: head/biology/bedtools/distinfo
==============================================================================
--- head/biology/bedtools/distinfo Sun Jan 24 18:15:20 2021 (r562500)
+++ head/biology/bedtools/distinfo Sun Jan 24 18:25:39 2021 (r562501)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1576701335
-SHA256 (arq5x-bedtools2-v2.29.2_GH0.tar.gz) = bc2f36b5d4fc9890c69f607d54da873032628462e88c545dd633d2c787a544a5
-SIZE (arq5x-bedtools2-v2.29.2_GH0.tar.gz) = 20638840
+TIMESTAMP = 1611493289
+SHA256 (arq5x-bedtools2-v2.30.0_GH0.tar.gz) = c575861ec746322961cd15d8c0b532bb2a19333f1cf167bbff73230a7d67302f
+SIZE (arq5x-bedtools2-v2.30.0_GH0.tar.gz) = 20639858
Modified: head/biology/bedtools/files/patch-Makefile
==============================================================================
--- head/biology/bedtools/files/patch-Makefile Sun Jan 24 18:15:20 2021 (r562500)
+++ head/biology/bedtools/files/patch-Makefile Sun Jan 24 18:25:39 2021 (r562501)
@@ -1,33 +1,36 @@
---- Makefile.orig 2019-09-07 21:14:56 UTC
+--- Makefile.orig 2021-01-23 19:33:26 UTC
+++ Makefile
-@@ -4,7 +4,7 @@
+@@ -4,7 +4,8 @@
# (c) 2009 Aaron Quinlan
# ==========================
-SHELL := /bin/bash -e
++# Use sh for portability and avoid bash extensions in shell commands
+SHELL := /bin/sh -e
VERSION_FILE=./src/utils/version/version_git.h
RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
-@@ -20,7 +20,7 @@ OBJ_DIR = obj
+@@ -21,7 +22,8 @@ OBJ_DIR = obj
BIN_DIR = bin
SRC_DIR = src
-CXX = g++
++# Default if not provided via the environment or make args
+CXX ?= g++
ifeq ($(DEBUG),1)
BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
-@@ -40,7 +40,7 @@ endif
+@@ -41,7 +43,8 @@ endif
BT_LDFLAGS =
BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
-prefix ?= /usr/local
++# Default if not provided via the environment or make args
+PREFIX ?= /usr/local
SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/bamToBed \
-@@ -183,9 +183,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+@@ -197,9 +200,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
.PHONY: all
install: all
Added: head/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp Sun Jan 24 18:25:39 2021 (r562501)
@@ -0,0 +1,23 @@
+--- src/utils/BamTools/include/SamHeader.hpp.orig 2021-01-24 16:15:06 UTC
++++ src/utils/BamTools/include/SamHeader.hpp
+@@ -7,6 +7,7 @@
+ #include <string.h>
+ #include <api/BamAux.h>
+ #include <stdlib.h>
++#include <sysexits.h>
+
+
+ #ifdef WITH_HTS_CB_API
+@@ -29,7 +30,11 @@ namespace htslib_future {
+ ops.cb_data = buffer;
+ samFile* fp = hts_open_callback(NULL, &ops, "w");
+
+- sam_hdr_write(fp, hdr);
++ if ( sam_hdr_write(fp, hdr) != 0 )
++ {
++ fputs("sam_hdr_rebuild: Error: sam_hdr_write() failed.\n", stderr);
++ exit(EX_IOERR);
++ }
+
+ hts_close(fp);
+
Modified: head/biology/bedtools/files/patch-src_utils_htslib_Makefile
==============================================================================
--- head/biology/bedtools/files/patch-src_utils_htslib_Makefile Sun Jan 24 18:15:20 2021 (r562500)
+++ head/biology/bedtools/files/patch-src_utils_htslib_Makefile Sun Jan 24 18:25:39 2021 (r562501)
@@ -1,27 +1,32 @@
---- src/utils/htslib/Makefile.orig 2019-03-25 03:58:18 UTC
+--- src/utils/htslib/Makefile.orig 2021-01-23 19:33:26 UTC
+++ src/utils/htslib/Makefile
-@@ -22,9 +22,9 @@
+@@ -22,20 +22,23 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
-CC = gcc
-AR = ar
-RANLIB = ranlib
++# Defaults if not provided by the environment or make args
+CC ?= gcc
+AR ?= ar
+RANLIB ?= ranlib
# Default libraries to link if configure is not used
htslib_default_libs = -lz -lm -lbz2 -llzma
-@@ -33,9 +33,9 @@ CPPFLAGS =
+
+-CPPFLAGS =
++# Defaults if not provided by the environment or make args
++CPPFLAGS ?=
++CFLAGS ?= -g -Wall -O2
++LDFLAGS ?=
++
# 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 -D__FUNCTION__=__func__
-CFLAGS = -g -Wall -O2
-+CFLAGS ?= -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS =
-+LDFLAGS ?=
LIBS = $(htslib_default_libs)
prefix = /usr/local
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