Date: Fri, 13 Sep 2019 13:21:59 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r511958 - in head/biology/bedtools: . files Message-ID: <201909131321.x8DDLxPE075162@repo.freebsd.org>
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Author: jwb Date: Fri Sep 13 13:21:59 2019 New Revision: 511958 URL: https://svnweb.freebsd.org/changeset/ports/511958 Log: biology/bedtools: Upgrade to 2.29.0 Add test target to run test scripts in dist Reported by: portscout Added: head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h (contents, props changed) head/biology/bedtools/files/patch-src_utils_htslib_Makefile (contents, props changed) Modified: head/biology/bedtools/Makefile head/biology/bedtools/distinfo head/biology/bedtools/files/patch-Makefile Modified: head/biology/bedtools/Makefile ============================================================================== --- head/biology/bedtools/Makefile Fri Sep 13 13:17:26 2019 (r511957) +++ head/biology/bedtools/Makefile Fri Sep 13 13:21:59 2019 (r511958) @@ -1,10 +1,9 @@ # $FreeBSD$ -PORTNAME= bedtools +PORTNAME= bedtools DISTVERSIONPREFIX= v -DISTVERSION= 2.27.1 -PORTREVISION= 3 -CATEGORIES= biology +DISTVERSION= 2.29.0 +CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Toolset for genome set arithmetic such as intersect, union @@ -12,6 +11,8 @@ COMMENT= Toolset for genome set arithmetic such as int LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE +TEST_DEPENDS= bash:shells/bash + USES= compiler:c++11-lang gmake python USE_GITHUB= yes GH_ACCOUNT= arq5x @@ -22,15 +23,17 @@ post-extract: @${MV} ${WRKSRC}/src/utils/gzstream/version \ ${WRKSRC}/src/utils/gzstream/version.txt -pre-build: +pre-configure: @${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile @${REINPLACE_CMD} -e 's|@\$$(CXX)|$$(CXX)|g' \ ${WRKSRC}/*/Makefile \ ${WRKSRC}/*/*/Makefile \ - ${WRKSRC}/*/*/*/Makefile \ - ${WRKSRC}/*/*/*/*/Makefile + ${WRKSRC}/*/*/*/Makefile post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools + +do-test: + (cd ${WRKSRC}/test && bash test.sh) .include <bsd.port.mk> Modified: head/biology/bedtools/distinfo ============================================================================== --- head/biology/bedtools/distinfo Fri Sep 13 13:17:26 2019 (r511957) +++ head/biology/bedtools/distinfo Fri Sep 13 13:21:59 2019 (r511958) @@ -1,3 +1,3 @@ -TIMESTAMP = 1519746174 -SHA256 (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112 -SIZE (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = 20003119 +TIMESTAMP = 1567891084 +SHA256 (arq5x-bedtools2-v2.29.0_GH0.tar.gz) = 8a13b7ec93a2dc960616268d8009f6061bec5a32b8a38d5734f80e851bb8ed1e +SIZE (arq5x-bedtools2-v2.29.0_GH0.tar.gz) = 20635364 Modified: head/biology/bedtools/files/patch-Makefile ============================================================================== --- head/biology/bedtools/files/patch-Makefile Fri Sep 13 13:17:26 2019 (r511957) +++ head/biology/bedtools/files/patch-Makefile Fri Sep 13 13:21:59 2019 (r511958) @@ -1,4 +1,4 @@ ---- Makefile.orig 2017-12-14 17:15:02 UTC +--- Makefile.orig 2019-09-07 21:14:56 UTC +++ Makefile @@ -4,7 +4,7 @@ # (c) 2009 Aaron Quinlan @@ -9,42 +9,25 @@ VERSION_FILE=./src/utils/version/version_git.h RELEASED_VERSION_FILE=./src/utils/version/version_release.txt -@@ -16,11 +16,11 @@ export OBJ_DIR = obj - export BIN_DIR = bin - export SRC_DIR = src - export UTIL_DIR = src/utils --export CXX = g++ -+export CXX ?= g++ - ifeq ($(DEBUG),1) --export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) -+export CXXFLAGS += -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) - else --export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) -+export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) - endif +@@ -20,7 +20,7 @@ OBJ_DIR = obj + BIN_DIR = bin + SRC_DIR = src - # If the user has specified to do so, tell the compile to use rand() (instead of mt19937). -@@ -33,7 +33,7 @@ endif - export LIBS = -lz - export BT_ROOT = src/utils/BamTools/ +-CXX = g++ ++CXX ?= g++ + ifeq ($(DEBUG),1) + BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +@@ -40,7 +40,7 @@ endif + BT_LDFLAGS = + BT_LIBS = -lz -lm -lbz2 -llzma -lpthread + -prefix ?= /usr/local +PREFIX ?= /usr/local SUBDIRS = $(SRC_DIR)/annotateBed \ $(SRC_DIR)/bamToBed \ -@@ -143,8 +143,8 @@ INCLUDES = -I$(SRC_DIR)/utils/bedFile \ - - all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS) - @echo "- Building main bedtools binary." -- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) -- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES) -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES) - @echo "done." - - @echo "- Creating executables for old CLI." -@@ -156,9 +156,9 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR) +@@ -183,9 +183,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR) .PHONY: all install: all @@ -56,12 +39,3 @@ done print_banner: -@@ -193,7 +193,7 @@ clean: - .PHONY: clean - - test: all -- @cd test; bash test.sh -+ @cd test; $(SHELL) test.sh - - .PHONY: test - Added: head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h Fri Sep 13 13:21:59 2019 (r511958) @@ -0,0 +1,11 @@ +--- src/utils/Contexts/ContextBase.h.orig 2019-03-25 18:03:45 UTC ++++ src/utils/Contexts/ContextBase.h +@@ -44,7 +44,7 @@ public: + FileRecordMgr *getFile(int fileIdx) { return _files[fileIdx]; } + void setProgram(PROGRAM_TYPE program) { _program = program; } + +- void addInputFile(const string &inputFile) { _fileNames.push_back(inputFile); } ++ void addInputFile(const string &inputFile) { _fileNames.push_back(inputFile); cerr << "Adding " << inputFile << endl; } + + int getNumInputFiles() const { return _fileNames.size(); } + const string &getInputFileName(int fileNum) const { return _fileNames[fileNum]; } Added: head/biology/bedtools/files/patch-src_utils_htslib_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bedtools/files/patch-src_utils_htslib_Makefile Fri Sep 13 13:21:59 2019 (r511958) @@ -0,0 +1,27 @@ +--- src/utils/htslib/Makefile.orig 2019-03-25 03:58:18 UTC ++++ src/utils/htslib/Makefile +@@ -22,9 +22,9 @@ + # 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 +@@ -33,9 +33,9 @@ CPPFLAGS = + # 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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