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-rw-r--r--sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch257
-rw-r--r--sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch16
2 files changed, 0 insertions, 273 deletions
diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch
deleted file mode 100644
index 238541b512f2..000000000000
--- a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch
+++ /dev/null
@@ -1,257 +0,0 @@
---- a/kmer/configure.sh
-+++ b/kmer/configure.sh
-@@ -254,13 +254,13 @@
- # -*- makefile -*-
- # Linux, optimized
- CC := $CC
--SHLIB_FLAGS := -shared
--CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--CLDFLAGS := -L/usr/local/lib
-+SHLIB_FLAGS := -shared ${LDFLAGS}
-+CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
-+CLDFLAGS :=
- CLIBS := -pthread -ldl
- CXX := $CXX
--CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--CXXLDFLAGS := -L/usr/local/lib
-+CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
-+CXXLDFLAGS :=
- CXXLIBS := -pthread -ldl
- ARFLAGS := ruvs
- INSTALL/ := $target/
-@@ -272,13 +272,13 @@
- # -*- makefile -*-
- # Linux64, optimized
- CC := $CC
--SHLIB_FLAGS := -shared
--CFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--CLDFLAGS := -L/usr/local/lib
-+SHLIB_FLAGS := -shared ${LDFLAGS}
-+CFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
-+CLDFLAGS :=
- CLIBS := -pthread -ldl
- CXX := $CXX
--CXXFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--CXXLDFLAGS := -L/usr/local/lib
-+CXXFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
-+CXXLDFLAGS :=
- CXXLIBS := -pthread -ldl
- ARFLAGS := ruvs
- INSTALL/ := $target/
-@@ -401,8 +401,8 @@
- .O := .o
- CLD := \${CC}
- CXXLD := \${CXX}
--CCDEP := gcc -MM -MG
--CXXDEP := g++ -MM -MG
-+CCDEP := \$(CC) -MM -MG
-+CXXDEP := \$(CXX) -MM -MG
- CLIBS += -lm -lbz2
- CXXLIBS += -lm -lbz2
- PYTHON := $PYTHON
---- a/kmer/Make.rules
-+++ b/kmer/Make.rules
-@@ -139,12 +139,12 @@
- ## EXE targets
- ALL_C_EXES :=$(strip $(foreach x,${//},${${x:.=.C_EXES}}))
- ${ALL_C_EXES}:
-- ${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS}
-+ ${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS}
- __SUBGOALS__+=$${${1:.=.C_EXES}}
-
- ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}}))
- ${ALL_CXX_EXES}:
-- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS}
-+ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS}
- __SUBGOALS__+=$${${1:.=.CXX_EXES}}
-
- define .RULE-install-copy-C-CXX-EXES
---- a/src/c_make.as
-+++ b/src/c_make.as
-@@ -64,27 +64,27 @@
-
- ifeq ($(OSTYPE), Linux)
- ifeq ($(MACHINETYPE), i686)
-- ARCH_LDFLAGS += -pthread -lm
-- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
-+ LINK_LIBS += -pthread -lm
-+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
- ARCH_LIB = /usr/X11R6/lib
- endif
- ifeq ($(MACHINETYPE), amd64)
-- ARCH_LDFLAGS += -pthread -lm
-- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
-+ LINK_LIBS += -pthread -lm
-+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
- ARCH_LIB = /usr/lib64 /usr/X11R6/lib64
- endif
- ifeq ($(MACHINETYPE), ia64)
-- ARCH_LDFLAGS += -pthread -lm
-- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-+ LINK_LIBS += -pthread -lm
-+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
- ARCH_LIB = /usr/X11R6/lib
- endif
-
- ifeq ($(BUILDDEBUG), 1)
-- ARCH_CFLAGS += -g
-- ARCH_LDFLAGS +=
-+ ARCH_CFLAGS +=
-+ LINK_LIBS +=
- else
-- ARCH_CFLAGS += -O2
-- ARCH_LDFLAGS += -Wl,-O1
-+ ARCH_CFLAGS +=
-+ LINK_LIBS +=
- endif
- endif
-
-@@ -94,19 +94,19 @@
-
- ifeq ($(OSTYPE), FreeBSD)
- ifeq ($(MACHINETYPE), i386)
-- ARCH_LDFLAGS += -pthread -lthr -lm
-- ARCH_CFLAGS = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
-- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
-+ LINK_LIBS += -pthread -lthr -lm
-+ ARCH_CFLAGS = -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
-+ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
- endif
- ifeq ($(MACHINETYPE), amd64)
-- ARCH_LDFLAGS += -pthread -lthr -lm
-- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
-- ARCH_CFLAGS = -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
-+ LINK_LIBS += -pthread -lthr -lm
-+ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
-+ ARCH_CFLAGS = -pthread -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
- endif
-
- ifeq ($(BUILDCOVERAGE), 1)
- ARCH_CFLAGS += -g -fprofile-arcs -ftest-coverage
-- ARCH_LDFLAGS += -lgcov
-+ LINK_LIBS += -lgcov
- else
- ifeq ($(BUILDDEBUG), 1)
- ARCH_CFLAGS += -g
-@@ -126,8 +126,6 @@
-
-
- ifeq ($(OSTYPE), Darwin)
-- CC = gcc
-- CXX = g++
- ARCH_CFLAGS = -D_THREAD_SAFE
-
- ifeq ($(MACHINETYPE), ppc)
-@@ -140,14 +138,14 @@
-
- ifeq ($(MACHINETYPE), i386)
- ifeq ($(BUILDDEBUG), 1)
-- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
-- ARCH_LDFLAGS += -m64 -lm
-+ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
-+ LINK_LIBS += -m64 -lm
- else
- # Wow, -Wshorten-64-to-32 is tough
-- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
-+ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
- # ARCH_CFLAGS += -Wextra
- # ARCH_CFLAGS += -pedantic (see above about pedantic)
-- ARCH_LDFLAGS += -m64 -lm
-+ LINK_LIBS += -m64 -lm
- endif
- endif
-
-@@ -161,23 +159,23 @@
- ifeq ($(OSTYPE), SunOS)
- ifeq ($(MACHINETYPE), i86pc)
- ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
-- ARCH_LDFLAGS += -lm
-+ LINK_LIBS += -lm
- endif
-
- ifeq ($(MACHINETYPE), sparc32)
- ARCH_CFLAGS = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
-- ARCH_LDFLAGS += -lm -lnsl -lsocket
-+ LINK_LIBS += -lm -lnsl -lsocket
- endif
-
- ifeq ($(MACHINETYPE), sparc64)
- ARCH_CFLAGS = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
-- ARCH_LDFLAGS += -m64 -lm -lnsl -lsocket
-+ LINK_LIBS += -lm -lnsl -lsocket
- endif
-
- ifeq ($(BUILDDEBUG), 1)
-- ARCH_CFLAGS += -g
-+ ARCH_CFLAGS +=
- else
-- ARCH_CFLAGS += -O
-+ ARCH_CFLAGS +=
- endif
- endif
-
-@@ -186,14 +184,14 @@
-
- ifeq ($(BUILDPROFILE), 1)
- ARCH_CFLAGS += -pg
-- ARCH_LDFLAGS += -pg
-+ LINK_LIBS += -pg
- endif
-
- # One can argue that CXXFLAGS should be separate. For now, we only
- # add to the flags.
-
- CFLAGS += $(ARCH_CFLAGS)
--CXXFLAGS += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS)
-+CXXFLAGS += $(ARCH_CXXFLAGS)
- LDFLAGS += $(ARCH_LDFLAGS)
-
- INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS)))
-@@ -205,7 +203,7 @@
- OBJ_SEARCH_PATH = $(LOCAL_OBJ)
-
- ifeq ($(SITE_NAME), JCVI)
-- LDFLAGS += -lcurl
-+ LINK_LIBS += -lcurl
- endif
-
- # The order of compilation here is very carefully chosen to be the
---- a/src/c_make.gen
-+++ b/src/c_make.gen
-@@ -248,10 +248,6 @@
- #### Do not redefine if (a) passed in on command line, or (b)
- #### defined in an environment variable.
-
--ifneq "$(origin CC)" "environment"
--CC=gcc
--endif
--
- ifneq "$(origin CPPFLAGS)" "environment"
- CPPFLAGS=
- endif
-@@ -264,10 +260,6 @@
- CDEFS=
- endif
-
--ifneq "$(origin CXX)" "environment"
--CXX=g++
--endif
--
- ifneq "$(origin CXXFLAGS)" "environment"
- CXXFLAGS=
- endif
-@@ -396,12 +388,12 @@
- $(C_PROGS):
- @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
- cd $(LOCAL_OBJ); \
-- $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
-+ $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
-
- $(CXX_PROGS):
- @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
- cd $(LOCAL_OBJ); \
-- $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
-+ $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
-
- $(SCRIPT_PROGS): %.sh:
- @echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch
deleted file mode 100644
index 7269b0b73c48..000000000000
--- a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff -ruN wgs-7.0.orig/src/c_make.as wgs-7.0/src/c_make.as
---- wgs-7.0.orig/src/c_make.as 2018-04-29 23:00:02.200181987 +0200
-+++ wgs-7.0/src/c_make.as 2018-04-29 23:17:33.612700507 +0200
-@@ -196,6 +196,12 @@
- CXXFLAGS += $(ARCH_CXXFLAGS)
- LDFLAGS += $(ARCH_LDFLAGS)
-
-+# libtirpc
-+
-+CFLAGS += -I/usr/include/tirpc
-+CXXFLAGS += -I/usr/include/tirpc
-+LINK_LIBS += -ltirpc
-+
- INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS)))
- INC_IMPORT_DIRS += $(ARCH_INC)
-
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-03 11:27:51 +0000