Attachment 211233 Details for Bug 243718 – svn diff for biology/stringtie to 2.1.1

[patch] svn diff for biology/stringtie to 2.1.1

stringtie-2.1.1.diff (text/plain), 5.73 KB, created by Motomichi Matsuzaki on 2020-02-01 05:05:29 UTC

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Creator: Motomichi Matsuzaki

Created: 2020-02-01 05:05:29 UTC

Size: 5.73 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 524625)
>+++ Makefile	(working copy)
>@@ -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=	${WRKSRC}/LICENSE
> 
>+TEST_DEPENDS=	bash:shells/bash \
>+		curl:ftp/curl
>+
> USES=		gmake
> ALL_TARGET=	release
>+TEST_TARGET=	test
> 
> PLIST_FILES=	bin/stringtie
> 
>Index: distinfo
>===================================================================
>--- distinfo	(revision 524625)
>+++ distinfo	(working copy)
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1530582079
>-SHA256 (stringtie-1.3.4d.tar.gz) = b1962d0108146ce7fea39d069b5e5de918e0e21daef9e1425ec9b778094d6ae6
>-SIZE (stringtie-1.3.4d.tar.gz) = 438025
>+TIMESTAMP = 1580533096
>+SHA256 (stringtie-2.1.1.tar.gz) = 7ea152b791856b1bd5dd2d475b06fae05398ee7e03f2f9844418010376edcca2
>+SIZE (stringtie-2.1.1.tar.gz) = 1969917
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 524625)
>+++ files/patch-Makefile	(working copy)
>@@ -1,55 +1,15 @@
>---- Makefile.orig	2018-03-06 16:29:49 UTC
>+--- Makefile.orig	2020-01-26 03:31:12 UTC
> +++ Makefile
>-@@ -6,12 +6,12 @@ GDIR      :=./gclib
>- 
>- INCDIRS   := -I. -I${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:
>Index: files/patch-gclib_GIntHash.hh
>===================================================================
>--- files/patch-gclib_GIntHash.hh	(revision 524625)
>+++ files/patch-gclib_GIntHash.hh	(nonexistent)
>@@ -1,20 +0,0 @@
>---- gclib/GIntHash.hh.orig	2018-03-06 16:29:49 UTC
>-+++ gclib/GIntHash.hh
>-@@ -122,7 +122,7 @@ public:
>-   uint32 NextKey() {
>-      Cell* cell=ghash.NextCell();
>-      if (cell) return cell->key;
>--       else return NULL;
>-+       else return 0;
>-   }
>-   OBJ* NextValue() {
>-      Cell* cell=ghash.NextCell();
>-@@ -201,7 +201,7 @@ public:
>-   uint32 NextKey() {
>-      Cell* cell=ghash.NextCell();
>-      if (cell) return cell->key;
>--       else return NULL;
>-+       else return 0;
>-   }
>-   OBJ* NextValue() {
>-      Cell* cell=ghash.NextCell();
>
>Property changes on: files/patch-gclib_GIntHash.hh
>___________________________________________________________________
>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: files/patch-samtools-0.1.18_bam__aux.c
>===================================================================
>--- files/patch-samtools-0.1.18_bam__aux.c	(revision 524625)
>+++ files/patch-samtools-0.1.18_bam__aux.c	(nonexistent)
>@@ -1,20 +0,0 @@
>---- samtools-0.1.18/bam_aux.c.orig	2018-03-06 16:29:49 UTC
>-+++ samtools-0.1.18/bam_aux.c
>-@@ -25,7 +25,7 @@ uint8_t *bam_aux_get_core(bam1_t *b, con
>- 	return bam_aux_get(b, tag);
>- }
>- 
>--inline int aux_type2size(uint8_t type)
>-+int aux_type2size(uint8_t type)
>- {
>-     switch (type) {
>-     case 'A': case 'c': case 'C':
>-@@ -43,7 +43,7 @@ inline int aux_type2size(uint8_t type)
>-     }
>- }
>- 
>--inline uint8_t* skip_aux(uint8_t* s) {
>-+uint8_t* skip_aux(uint8_t* s) {
>- 	int size = aux_type2size(*s); ++s; // skip type
>- 	uint32_t n;
>- 	switch (size) {
>
>Property changes on: files/patch-samtools-0.1.18_bam__aux.c
>___________________________________________________________________
>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

Flags:

mzaki: maintainer-approval+

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Attachments on bug 243718: 211182 | 211233