Index: head/biology/bedtools/Makefile =================================================================== --- head/biology/bedtools/Makefile (revision 562500) +++ head/biology/bedtools/Makefile (revision 562501) @@ -1,39 +1,31 @@ # $FreeBSD$ PORTNAME= bedtools DISTVERSIONPREFIX= v -DISTVERSION= 2.29.2 +DISTVERSION= 2.30.0 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Toolset for genome set arithmetic such as intersect, union LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE TEST_DEPENDS= bash:shells/bash USES= compiler:c++11-lang gmake python USE_GITHUB= yes + GH_ACCOUNT= arq5x GH_PROJECT= bedtools2 -post-extract: -# Avoid conflict with C++20 by adding .txt suffix - @${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 do-test: (cd ${WRKSRC}/test && bash test.sh) .include Index: head/biology/bedtools/distinfo =================================================================== --- head/biology/bedtools/distinfo (revision 562500) +++ head/biology/bedtools/distinfo (revision 562501) @@ -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 Index: head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h =================================================================== --- head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h (revision 562500) +++ head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h (nonexistent) @@ -1,11 +0,0 @@ ---- 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]; } Property changes on: head/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/bedtools/files/patch-Makefile =================================================================== --- head/biology/bedtools/files/patch-Makefile (revision 562500) +++ head/biology/bedtools/files/patch-Makefile (revision 562501) @@ -1,41 +1,44 @@ ---- 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 - mkdir -p $(DESTDIR)$(prefix)/bin + mkdir -p $(DESTDIR)$(PREFIX)/bin for file in bin/* ; do \ - cp -f $$file $(DESTDIR)$(prefix)/bin; \ + cp -f $$file $(DESTDIR)$(PREFIX)/bin; \ done print_banner: Index: head/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp =================================================================== --- head/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp (nonexistent) +++ head/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp (revision 562501) @@ -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 + #include + #include ++#include + + + #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); + Property changes on: head/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/bedtools/files/patch-src_utils_htslib_Makefile =================================================================== --- head/biology/bedtools/files/patch-src_utils_htslib_Makefile (revision 562500) +++ head/biology/bedtools/files/patch-src_utils_htslib_Makefile (revision 562501) @@ -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