Attachment #194846 for bug #229480

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# $FreeBSD$

PORTNAME=	stringtie
PORTVERSION=	1.3.4d
CATEGORIES=	biology
MASTER_SITES=	http://ccb.jhu.edu/software/stringtie/dl/

MAINTAINER=	mzaki@niid.go.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

USES=		gmake

ALL_TARGET=	release

PLIST_FILES=	bin/stringtie

do-install:
	${INSTALL_PROGRAM} ${WRKSRC}/stringtie ${STAGEDIR}${PREFIX}/bin

.include <bsd.port.mk>

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(-)distinfo (+3 lines)
	1	TIMESTAMP = 1530582079
	2	SHA256 (stringtie-1.3.4d.tar.gz) = b1962d0108146ce7fea39d069b5e5de918e0e21daef9e1425ec9b778094d6ae6
	3	SIZE (stringtie-1.3.4d.tar.gz) = 438025




--- Makefile.orig	2018-03-06 16:29:49 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
 endif
 
 #detect MinGW (Windows environment)
-ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
+ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
  WINDOWS=1
 endif
 
 # 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
 
 
 %.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
 tmerge.o : rlink.h tmerge.h
 tablemaker.o : tablemaker.h rlink.h
 ${BAM}/libbam.a: 
-	cd ${BAM} && make lib
+	cd ${BAM} && ${MAKE} lib
 stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
 	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
 	@echo
@@ -151,6 +151,6 @@ clean:
 	${RM} stringtie${EXE} stringtie.o*  $(OBJS)
 	${RM} core.*
 allclean cleanAll cleanall:
-	cd ${BAM} && make clean
+	cd ${BAM} && ${MAKE} clean
 	${RM} stringtie${EXE} stringtie.o* $(OBJS)
 	${RM} core.*




--- 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();

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(-)files/patch-samtools-0.1.18_Makefile (+10 lines)
	1	--- samtools-0.1.18/Makefile.orig 2018-03-06 16:29:49 UTC
	2	+++ samtools-0.1.18/Makefile
	3	@@ -1,5 +1,5 @@
	4	-CC= gcc
	5	-CFLAGS= -g -Wall -fsigned-char -O2 #-m64 #-arch ppc
	6	+CC?= gcc
	7	+CFLAGS?= -g -Wall -fsigned-char -O2 #-m64 #-arch ppc
	8	DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 #-D_USE_KNETFILE
	9	KNETFILE_O= knetfile.o
	10	LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \




--- 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) {

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(-)pkg-descr (+11 lines)
	1	StringTie is a fast and highly efficient assembler of RNA-seq alignments into
	2	potential transcripts. The input can be the alignments of raw reads as usual;
	3	it also accepts longer assembled sequences. The output can be processed by
	4	downstream software including Ballgown, Cuffdiff, etc.
	5
	6	Citation:
	7	Pertea et al. (2015) StringTie enables improved reconstruction of a
	8	transcriptome from RNA-seq reads.
	9	Nature Biotechnology 33: 290-295 doi:10.1038/nbt.3122
	10
	11	WWW: http://www.ccb.jhu.edu/software/stringtie/

Return to bug 229480

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(-)Makefile (+25 lines)
	1	# $FreeBSD$
	2
	3	PORTNAME= stringtie
	4	PORTVERSION= 1.3.4d
	5	CATEGORIES= biology
	6	MASTER_SITES= http://ccb.jhu.edu/software/stringtie/dl/
	7
	8	MAINTAINER= mzaki@niid.go.jp
	9	COMMENT= Transcript assembly and quantification for RNA-seq
	10
	11	LICENSE= ART20 MIT
	12	LICENSE_COMB= multi
	13	LICENSE_FILE_ART20= ${WRKSRC}/LICENSE
	14	LICENSE_FILE_MIT= ${WRKSRC}/samtools-0.1.18/COPYING
	15
	16	USES= gmake
	17
	18	ALL_TARGET= release
	19
	20	PLIST_FILES= bin/stringtie
	21
	22	do-install:
	23	${INSTALL_PROGRAM} ${WRKSRC}/stringtie ${STAGEDIR}${PREFIX}/bin
	24
	25	.include <bsd.port.mk>

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(-)files/patch-Makefile (+68 lines)
		1	--- Makefile.orig 2018-03-06 16:29:49 UTC
		2	+++ Makefile
		3	@@ -6,12 +6,12 @@ GDIR :=./gclib
		4
		5	INCDIRS := -I. -I${GDIR} -I${BAM}
		6
		7	-CC := g++
		8	+CXX ?= g++
		9
		10	BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
		11	-D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti
		12
		13	-LINKER := g++
		14	+LINKER = ${CXX}
		15
		16	LDFLAGS := -g -L${BAM} $(LDFLAGS)
		17
		18	@@ -22,13 +22,13 @@ ifneq (,$(findstring nothreads,$(MAKECMD
		19	endif
		20
		21	#detect MinGW (Windows environment)
		22	-ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
		23	+ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
		24	WINDOWS=1
		25	endif
		26
		27	# MinGW32 GCC 4.5 link problem fix
		28	#ifdef WINDOWS
		29	-ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion)))
		30	+ifneq (,$(findstring 4.5.,$(shell ${CXX} -dumpversion)))
		31	STATIC_CLIB=1
		32	endif
		33	#endif
		34	@@ -63,7 +63,7 @@ endif
		35	ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
		36	# -- release build
		37	RELEASE_BUILD=1
		38	- CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3
		39	+ CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS)
		40	else
		41	ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
		42	#use sanitizer in gcc 4.9+
		43	@@ -122,7 +122,7 @@ endif
		44
		45
		46	%.o : %.cpp
		47	- ${CC} ${CFLAGS} -c $< -o $@
		48	+ ${CXX} ${CFLAGS} -c $< -o $@
		49
		50	OBJS += rlink.o tablemaker.o tmerge.o
		51
		52	@@ -137,7 +137,7 @@ rlink.o : rlink.h tablemaker.h $(GDIR)/G
		53	tmerge.o : rlink.h tmerge.h
		54	tablemaker.o : tablemaker.h rlink.h
		55	${BAM}/libbam.a:
		56	- cd ${BAM} && make lib
		57	+ cd ${BAM} && ${MAKE} lib
		58	stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
		59	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
		60	@echo
		61	@@ -151,6 +151,6 @@ clean:
		62	${RM} stringtie${EXE} stringtie.o* $(OBJS)
		63	${RM} core.*
		64	allclean cleanAll cleanall:
65	- cd ${BAM} && make clean
66	+ cd ${BAM} && ${MAKE} clean
67	${RM} stringtie${EXE} stringtie.o* $(OBJS)
68	${RM} core.*

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(-)files/patch-gclib_GIntHash.hh (+20 lines)
	1	--- gclib/GIntHash.hh.orig 2018-03-06 16:29:49 UTC
	2	+++ gclib/GIntHash.hh
	3	@@ -122,7 +122,7 @@ public:
	4	uint32 NextKey() {
	5	Cell* cell=ghash.NextCell();
	6	if (cell) return cell->key;
	7	- else return NULL;
	8	+ else return 0;
	9	}
	10	OBJ* NextValue() {
	11	Cell* cell=ghash.NextCell();
	12	@@ -201,7 +201,7 @@ public:
	13	uint32 NextKey() {
	14	Cell* cell=ghash.NextCell();
	15	if (cell) return cell->key;
	16	- else return NULL;
	17	+ else return 0;
	18	}
	19	OBJ* NextValue() {
	20	Cell* cell=ghash.NextCell();

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(-)files/patch-samtools-0.1.18_bam__aux.c (+20 lines)
	1	--- samtools-0.1.18/bam_aux.c.orig 2018-03-06 16:29:49 UTC
	2	+++ samtools-0.1.18/bam_aux.c
	3	@@ -25,7 +25,7 @@ uint8_t bam_aux_get_core(bam1_t b, con
	4	return bam_aux_get(b, tag);
	5	}
	6
	7	-inline int aux_type2size(uint8_t type)
	8	+int aux_type2size(uint8_t type)
	9	{
	10	switch (type) {
	11	case 'A': case 'c': case 'C':
	12	@@ -43,7 +43,7 @@ inline int aux_type2size(uint8_t type)
	13	}
	14	}
	15
	16	-inline uint8_t* skip_aux(uint8_t* s) {
	17	+uint8_t* skip_aux(uint8_t* s) {
	18	int size = aux_type2size(*s); ++s; // skip type
	19	uint32_t n;
	20	switch (size) {