1 files changed, 0 insertions, 112 deletions
diff --git a/sci-biology/stringtie/files/Makefile.patch b/sci-biology/stringtie/files/Makefile.patch
deleted file mode 100644
index b7efa605c..000000000
--- a/sci-biology/stringtie/files/Makefile.patch
+++ /dev/null
@@ -1,112 +0,0 @@
---- stringtie-1.3.4d/Makefile	2018-06-26 00:36:17.119583211 +0200
-+++ stringtie-1.3.4d/Makefile	2018-06-26 00:46:43.406712302 +0200
-@@ -1,28 +1,32 @@
--BAM := ./samtools-0.1.18
--#path to the directory where the samtools package was built (in place)
--#so libbam.a and *.h files MUST be in here
-+#-- for now these MUST point to the included samtools-0.x.x and gclib subdirectories
-+BAM  := ./samtools-0.1.18
-+GDIR := ./gclib
-+#--
- 
--GDIR      :=./gclib
-+INCDIRS := -I. -I${GDIR} -I${BAM}
- 
--INCDIRS   := -I. -I${GDIR} -I${BAM}
--
--CC        := g++
-+#CXX  ?= g++
-+CXX   := $(if $(CXX),$(CXX),g++)
- 
- BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
- -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti
-+#for gcc 8+ add: -Wno-class-memaccess
-+
-+
-+LINKER  := $(if $(LINKER),$(LINKER),g++)
- 
--LINKER    := g++
-+LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
- 
--LDFLAGS   := -g -L${BAM} $(LDFLAGS)
-+LDFLAGS += -L${BAM}
- 
--LIBS      := -lbam -lz
-+LIBS    := -lbam -lz
- 
- ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
-  NOTHREADS=1
- endif
- 
- #detect MinGW (Windows environment)
--ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
-+ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
-  WINDOWS=1
- endif
- 
-@@ -63,7 +67,8 @@ endif
- ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
-   # -- release build
-   RELEASE_BUILD=1
--  CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3
-+  CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O3)
-+  CXXFLAGS += -DNDEBUG $(BASEFLAGS)
- else
-   ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
-      #use sanitizer in gcc 4.9+
-@@ -72,21 +77,21 @@ else
-      ifeq "$(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)
-+     CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
-+     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 += -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)
-+     CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
-      LIBS := -lasan -lubsan -ldl $(LIBS)
-   else
--    ifeq (,$(findstring clean,$(MAKECMDGOALS)))
-      #just plain debug build
-      DEBUG_BUILD=1
--     CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
--    endif
-+     CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
-+     CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
-   endif
- endif
- 
-@@ -106,23 +111,20 @@ ifdef DEBUG_BUILD
-   DBG_WARN+='WARNING: built DEBUG version [much slower], use "make clean release" for a faster, optimized version of the program.'
- endif
- 
--
- OBJS := ${GDIR}/GBase.o ${GDIR}/GArgs.o ${GDIR}/GStr.o ${GDIR}/GBam.o \
-  ${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFaSeqGet.o ${GDIR}/gff.o 
- 
--
- ifneq (,$(filter %memtrace %memusage %memuse, $(MAKECMDGOALS)))
--    CFLAGS += -DGMEMTRACE
-+    CXXFLAGS += -DGMEMTRACE
-     OBJS += ${GDIR}/proc_mem.o
- endif
- 
- ifndef NOTHREADS
-  OBJS += ${GDIR}/GThreads.o 
- endif
- 
--
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- OBJS += rlink.o tablemaker.o tmerge.o
-