sci-biology/stringtie: patch cleanup

Package-Manager: Portage-2.3.40, Repoman-2.3.9

1 files changed, 28 insertions, 34 deletions

diff --git a/sci-biology/stringtie/files/Makefile.patch b/sci-biology/stringtie/files/Makefile.patch
index 8f5379b6b..7db068985 100644
--- a/sci-biology/stringtie/files/Makefile.patch
+++ b/sci-biology/stringtie/files/Makefile.patch
@@ -1,8 +1,8 @@
---- stringtie-1.2.2/Makefile	2018-06-25 23:28:55.558150677 +0200
-+++ stringtie-1.2.2/Makefile	2018-06-25 23:29:55.819798846 +0200
+--- stringtie-1.2.2/Makefile	2018-06-26 00:36:17.119583211 +0200
++++ stringtie-1.2.2/Makefile	2018-06-26 00:46:43.406712302 +0200
 @@ -1,13 +1,15 @@
 -BAM := ./samtools-0.1.18
-+BAM_INC = $(EPREFIX)/usr/include/bam-0.1-legacy
++BAM_INC = -I$(EPREFIX)/usr/include/bam-0.1-legacy
 +BAM_LIB =  # or -L/some/path
 +BAM_LIBS = -lbam-0.1-legacy
  #path to the directory where the samtools package was built (in place)
@@ -11,7 +11,7 @@
  GDIR :=./gclib
  
 -INCDIRS := -I. -I${GDIR} -I${BAM}
-+INCDIRS := -I. -I${GDIR} -I${BAM_INC}
++INCDIRS := -I. -I${GDIR} ${BAM_INC}
  
 -#CC := clang++
 -CC      := g++
@@ -20,7 +20,7 @@
  
  
  ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
-@@ -15,12 +17,12 @@
+@@ -15,7 +17,7 @@
  endif
  
  #detect MinGW (Windows environment)
@@ -29,69 +29,63 @@
   WINDOWS=1
  endif
  
- LFLAGS = 
--# MinGW32 GCC 4.5 link problem fix
-+# MinGW32 GCXX 4.5 link problem fix
- #ifdef WINDOWS
- ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion)))
-  LFLAGS += -static-libstdc++ -static-libgcc
-@@ -50,7 +52,7 @@
+@@ -48,9 +50,9 @@
+ # C/C++ linker
+ 
  #LINKER := clang++
- LINKER  := g++
+-LINKER  := g++
++LINKER  ?= g++
  
 -LIBS := -lbam -lz
 +LIBS := ${BAM_LIBS} -lz
  
  # Non-windows systems need pthread
  ifndef WINDOWS
-@@ -68,27 +70,27 @@
+@@ -68,8 +70,10 @@
  #ifneq (,$(findstring release,$(MAKECMDGOALS)))
  ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
    # -- release build
 -  CFLAGS := -O3 -DNDEBUG -g $(BASEFLAGS)
 -  LDFLAGS := -g -L${BAM} ${LFLAGS}
-+  CXXFLAGS += -DNDEBUG -g $(BASEFLAGS)
++  CXXFLAGS ?= -O3 -g
++  CXXFLAGS += -DNDEBUG $(BASEFLAGS)
++  LDFLAGS ?= -g
 +  LDFLAGS += ${BAM_LIB} ${LFLAGS}
    ifneq (,$(findstring static,$(MAKECMDGOALS)))
      LDFLAGS += -static-libstdc++ -static-libgcc
    endif
- else
-   ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
-      #make memcheck : use the statically linked address sanitizer in gcc 4.9.x
--     GCCVER49 := $(shell expr `g++ -dumpversion | cut -f1,2 -d.` \>= 4.9)
--     ifeq "$(GCCVER49)" "0"
-+     GCXXVER49 := $(shell expr `g++ -dumpversion | cut -f1,2 -d.` \>= 4.9)
-+     ifeq "$(GCXXVER49)" "0"
+@@ -80,15 +84,16 @@
+      ifeq "$(GCCVER49)" "0"
         $(error gcc version 4.9 or greater is required for this build target)
       endif
 -     CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS)
--     GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
--     ifeq "$(GCCVER5)" "1"
++     CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS)
+      GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
+      ifeq "$(GCCVER5)" "1"
 -       CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
 -       CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
 -       #CFLAGS += -fcheck-pointer-bounds -mmpx
-+     CXXFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS)
-+     GCXXVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
-+     ifeq "$(GCXXVER5)" "1"
 +       CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
 +       CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
 +       #CXXFLAGS += -fcheck-pointer-bounds -mmpx
       endif
 -     CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CFLAGS)
 -     LDFLAGS := -g -L${BAM}
-+     CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CXXFLAGS)
-+     LDFLAGS += ${BAM_LIB}
++     CXXFLAGS ?= -g
++     CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
++     LDFLAGS += -g ${BAM_LIB}
       #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS)
       LIBS := -lasan -lubsan -ldl $(LIBS)
    else
-@@ -97,13 +99,13 @@
+@@ -97,13 +102,14 @@
         GMEMTRACE=1
     endif
     #just plain debug build
 -    CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
 -    LDFLAGS := -g -L${BAM}
-+    CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-+    LDFLAGS += ${BAM_LIB}
++   CXXFLAGS ?= -g
++   CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
++   LDFLAGS += ${BAM_LIB}
    endif
  endif
  
@@ -101,7 +95,7 @@
  
  OBJS := ${GDIR}/GBase.o ${GDIR}/GArgs.o ${GDIR}/GStr.o ${GDIR}/GBam.o \
   ${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFaSeqGet.o ${GDIR}/gff.o 
-@@ -130,9 +132,7 @@
+@@ -130,9 +136,7 @@
  rlink.o : rlink.h tablemaker.h $(GDIR)/GBam.h $(GDIR)/GBitVec.h
  tmerge.o : rlink.h tmerge.h
  tablemaker.o : tablemaker.h rlink.h
@@ -112,7 +106,7 @@
  	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
  
  .PHONY : clean cleanall cleanAll allclean
-@@ -143,7 +143,6 @@
+@@ -143,7 +147,6 @@
  	@${RM} stringtie stringtie.o* stringtie.exe $(OBJS)
  	@${RM} core.*
  allclean cleanAll cleanall: