sci-biology/velvet: remove unused patch

Closes: https://github.com/gentoo/gentoo/pull/3708

diff --git a/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff b/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff
deleted file mode 100644 (file)
index 883211a..0000000
--- a/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff
+++ /dev/null
@@ -1,126 +0,0 @@
-Debundle zlib, fixes parallel build, respect user FLAGS
-
---- src/readSet.c
-+++ src/readSet.c
-@@ -23,18 +23,13 @@
- #include <string.h>
- #include <math.h>
- #include <time.h>
-+#include <zlib.h>
- 
- #include "globals.h"
- #include "tightString.h"
- #include "readSet.h"
- #include "utility.h"
- 
--#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
--#include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
--#else
--#include "../third-party/zlib-1.2.3/zlib.h"
--#endif
--
- #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
- #  include <fcntl.h>
- #  include <io.h>
-
---- Makefile
-+++ Makefile
-@@ -1,77 +1,62 @@
--CC = gcc
--CFLAGS = -Wall
--DEBUG = -g
--LDFLAGS = -lm
--OPT = -O3
-+LIBS = -lm -lz
- MAXKMERLENGTH=31
- CATEGORIES=2
- DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
- 
--Z_LIB_DIR=third-party/zlib-1.2.3
--Z_LIB_FILES=$(Z_LIB_DIR)/*.o
--
--# Mac OS users: uncomment the following lines
--# Z_LIB_FILES=
--# LDFLAGS = -lm -lz
--# CFLAGS = -Wall -m64
--
--# Sparc/Solaris users: uncomment the following line
--# CFLAGS = -Wall -m64
--
- OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/crc.o obj/utility.o obj/kmer.o obj/scaffold.o
- OBJDBG = $(subst obj,obj/dbg,$(OBJ))
-+OBJDE  = $(subst obj,objde,$(OBJ))
- 
--default : cleanobj zlib obj velveth velvetg doc
-+default : cleanobj  obj velveth velvetg 
- 
- clean :
--      -rm obj/*.o obj/dbg/*.o ./velvet* 
--      cd $(Z_LIB_DIR) && make clean
-+      -rm -f obj/*.o obj/dbg/*.o ./velvet* objde/*.o
-       -rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log
- 
- cleanobj: 
--      -rm obj/*.o obj/dbg/*.o 
--
--zlib : 
--      cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
-+      -rm -f obj/*.o obj/dbg/*.o objde/*.o
- 
- velveth : obj 
--      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(LIBS)
- 
- 
- velvetg : obj
--      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(LIBS)
- 
- debug : cleanobj obj/dbg
--      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
--      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS)
-+      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS)
- 
- color : cleanobj obj_de
--      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
--      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de objde/tightString.o objde/run.o objde/recycleBin.o objde/splay.o objde/splayTable.o objde/readSet.o objde/crc.o objde/utility.o objde/kmer.o $(LIBS)
-+      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de objde/tightString.o objde/graph.o objde/run2.o objde/fibHeap.o objde/fib.o objde/concatenatedGraph.o objde/passageMarker.o objde/graphStats.o objde/correctedGraph.o objde/dfib.o objde/dfibHeap.o objde/recycleBin.o objde/readSet.o objde/shortReadPairs.o objde/scaffold.o objde/locallyCorrectedGraph.o objde/graphReConstruction.o objde/roadMap.o objde/preGraph.o objde/preGraphConstruction.o objde/concatenatedPreGraph.o objde/readCoherentGraph.o objde/utility.o objde/kmer.o $(LIBS)
- 
- colordebug : cleanobj obj/dbg_de
--      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
--      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de objde/dbg/tightString.o objde/dbg/run.o objde/dbg/recycleBin.o objde/dbg/splay.o objde/dbg/splayTable.o objde/dbg/readSet.o objde/dbg/crc.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS)
-+      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de objde/dbg/tightString.o objde/dbg/graph.o objde/dbg/run2.o objde/dbg/fibHeap.o objde/dbg/fib.o objde/dbg/concatenatedGraph.o objde/dbg/passageMarker.o objde/dbg/graphStats.o objde/dbg/correctedGraph.o objde/dbg/dfib.o objde/dbg/dfibHeap.o objde/dbg/recycleBin.o objde/dbg/readSet.o objde/dbg/shortReadPairs.o objde/dbg/scaffold.o objde/dbg/locallyCorrectedGraph.o objde/dbg/graphReConstruction.o objde/dbg/roadMap.o objde/dbg/preGraph.o objde/dbg/preGraphConstruction.o objde/dbg/concatenatedPreGraph.o objde/dbg/readCoherentGraph.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS)
- 
- objdir:
-       mkdir -p obj
-+      mkdir -p objde
- 
--obj: zlib objdir $(OBJ)
-+obj:  objdir $(OBJ)
- 
--obj_de: override DEF := $(DEF) -D COLOR
--obj_de: zlib cleanobj objdir $(OBJ)
-+obj_de:  cleanobj objdir $(OBJDE)
- 
- obj/dbgdir: 
-       mkdir -p obj/dbg
- 
--obj/dbg: zlib obj/dbgdir $(OBJDBG)
-+obj/dbg: obj/dbgdir $(OBJDBG)
- 
- obj/dbg_de: override DEF := $(DEF) -D COLOR
--obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
-+obj/dbg_de: cleanobj obj/dbgdir $(OBJDBG)
- 
- obj/%.o: src/%.c
-       $(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ 
- 
-+objde/%.o: src/%.c
-+      $(CC) $(CFLAGS) $(OPT) $(DEF) -D COLOR -c $? -o $@ 
-+
- obj/dbg/%.o: src/%.c
-       $(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ 
-