Date: Sun, 16 Feb 2020 20:54:52 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r526322 - in head/biology/stringtie: . files Message-ID: <202002162054.01GKsq06014877@repo.freebsd.org>
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Author: yuri Date: Sun Feb 16 20:54:52 2020 New Revision: 526322 URL: https://svnweb.freebsd.org/changeset/ports/526322 Log: biology/stringtie: Update 1.3.4d -> 2.1.1 PR: 243718 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> (maintainer) Deleted: head/biology/stringtie/files/patch-gclib_GIntHash.hh head/biology/stringtie/files/patch-samtools-0.1.18_bam__aux.c Modified: head/biology/stringtie/Makefile head/biology/stringtie/distinfo head/biology/stringtie/files/patch-Makefile Modified: head/biology/stringtie/Makefile ============================================================================== --- head/biology/stringtie/Makefile Sun Feb 16 20:47:56 2020 (r526321) +++ head/biology/stringtie/Makefile Sun Feb 16 20:54:52 2020 (r526322) @@ -1,20 +1,22 @@ # $FreeBSD$ PORTNAME= stringtie -DISTVERSION= 1.3.4d +DISTVERSION= 2.1.1 CATEGORIES= biology MASTER_SITES= http://ccb.jhu.edu/software/stringtie/dl/ -MAINTAINER= mzaki@niid.go.jp +MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Transcript assembly and quantification for RNA-seq -LICENSE= ART20 MIT -LICENSE_COMB= multi -LICENSE_FILE_ART20= ${WRKSRC}/LICENSE -LICENSE_FILE_MIT= ${WRKSRC}/samtools-0.1.18/COPYING +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE +TEST_DEPENDS= bash:shells/bash \ + curl:ftp/curl + USES= gmake ALL_TARGET= release +TEST_TARGET= test PLIST_FILES= bin/stringtie Modified: head/biology/stringtie/distinfo ============================================================================== --- head/biology/stringtie/distinfo Sun Feb 16 20:47:56 2020 (r526321) +++ head/biology/stringtie/distinfo Sun Feb 16 20:54:52 2020 (r526322) @@ -1,3 +1,3 @@ -TIMESTAMP = 1530582079 -SHA256 (stringtie-1.3.4d.tar.gz) = b1962d0108146ce7fea39d069b5e5de918e0e21daef9e1425ec9b778094d6ae6 -SIZE (stringtie-1.3.4d.tar.gz) = 438025 +TIMESTAMP = 1580533096 +SHA256 (stringtie-2.1.1.tar.gz) = 7ea152b791856b1bd5dd2d475b06fae05398ee7e03f2f9844418010376edcca2 +SIZE (stringtie-2.1.1.tar.gz) = 1969917 Modified: head/biology/stringtie/files/patch-Makefile ============================================================================== --- head/biology/stringtie/files/patch-Makefile Sun Feb 16 20:47:56 2020 (r526321) +++ head/biology/stringtie/files/patch-Makefile Sun Feb 16 20:54:52 2020 (r526322) @@ -1,55 +1,15 @@ ---- Makefile.orig 2018-03-06 16:29:49 UTC +--- Makefile.orig 2020-01-26 03:31:12 UTC +++ Makefile -@@ -6,12 +6,12 @@ GDIR :=./gclib - - INCDIRS := -I. -I${GDIR} -I${BAM} - --CC := g++ -+CXX ?= g++ - - BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \ - -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti - --LINKER := g++ -+LINKER = ${CXX} - - LDFLAGS := -g -L${BAM} $(LDFLAGS) - -@@ -22,13 +22,13 @@ ifneq (,$(findstring nothreads,$(MAKECMD +@@ -20,7 +20,7 @@ ifeq "$(GCCVER8)" "1" + BASEFLAGS += -Wno-class-memaccess endif - #detect MinGW (Windows environment) --ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine))) -+ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine))) - WINDOWS=1 - endif +-LINKER := $(if $(LINKER),$(LINKER),g++) ++LINKER := $(if $(LINKER),$(LINKER),$(CXX)) - # MinGW32 GCC 4.5 link problem fix - #ifdef WINDOWS --ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion))) -+ifneq (,$(findstring 4.5.,$(shell ${CXX} -dumpversion))) - STATIC_CLIB=1 - endif - #endif -@@ -63,7 +63,7 @@ endif - ifneq (,$(filter %release %static, $(MAKECMDGOALS))) - # -- release build - RELEASE_BUILD=1 -- CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3 -+ CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) - else - ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS))) - #use sanitizer in gcc 4.9+ -@@ -122,7 +122,7 @@ endif + LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g) - - %.o : %.cpp -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CFLAGS} -c $< -o $@ - - OBJS += rlink.o tablemaker.o tmerge.o - -@@ -137,7 +137,7 @@ rlink.o : rlink.h tablemaker.h $(GDIR)/G +@@ -151,7 +151,7 @@ rlink.o : rlink.h tablemaker.h $(GDIR)/G tmerge.o : rlink.h tmerge.h tablemaker.o : tablemaker.h rlink.h ${BAM}/libbam.a: @@ -58,7 +18,7 @@ stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} @echo -@@ -151,6 +151,6 @@ clean: +@@ -167,6 +167,6 @@ clean: ${RM} stringtie${EXE} stringtie.o* $(OBJS) ${RM} core.* allclean cleanAll cleanall:
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