diff options
Diffstat (limited to 'sci-biology/mummer/files')
| -rw-r--r-- | sci-biology/mummer/files/3.22-ldflags.patch | 16 | ||||
| -rw-r--r-- | sci-biology/mummer/files/3.22-prll.patch | 56 | ||||
| -rw-r--r-- | sci-biology/mummer/files/mummer-3.20-gcc43.patch | 12 |
3 files changed, 84 insertions, 0 deletions
diff --git a/sci-biology/mummer/files/3.22-ldflags.patch b/sci-biology/mummer/files/3.22-ldflags.patch new file mode 100644 index 000000000000..d3c4a60a1adb --- /dev/null +++ b/sci-biology/mummer/files/3.22-ldflags.patch @@ -0,0 +1,16 @@ +diff --git a/src/tigr/Makefile b/src/tigr/Makefile +index cf6b9ca..5b28d1e 100644 +--- a/src/tigr/Makefile ++++ b/src/tigr/Makefile +@@ -9,9 +9,9 @@ AUX_BIN_DIR := $(CURDIR) + endif + + OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@ +-BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \ ++BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \ + chmod 755 $(BIN_DIR)/$@ +-AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \ ++AUX_BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \ + chmod 755 $(AUX_BIN_DIR)/$@ + VPATH := $(AUX_BIN_DIR):$(BIN_DIR) + diff --git a/sci-biology/mummer/files/3.22-prll.patch b/sci-biology/mummer/files/3.22-prll.patch new file mode 100644 index 000000000000..3b24ee40214a --- /dev/null +++ b/sci-biology/mummer/files/3.22-prll.patch @@ -0,0 +1,56 @@ +diff --git a/Makefile b/Makefile +index 4db4977..bbd00ed 100644 +--- a/Makefile ++++ b/Makefile +@@ -114,15 +114,15 @@ install: all + + + kurtz: +- cd $(KURTZ_SRC_DIR); $(MAKE) mummer ++ $(MAKE) -C $(KURTZ_SRC_DIR) mummer + + + scripts: +- cd $(SCRIPT_DIR); $(MAKE) all ++ $(MAKE) -C $(SCRIPT_DIR) all + + + tigr: +- cd $(TIGR_SRC_DIR); $(MAKE) all ++ $(MAKE) -C $(TIGR_SRC_DIR) all + + + uninstall: clean +diff --git a/src/kurtz/Makefile b/src/kurtz/Makefile +index 85dfc16..5bff793 100644 +--- a/src/kurtz/Makefile ++++ b/src/kurtz/Makefile +@@ -1,7 +1,7 @@ + all: +- cd libbasedir; $(MAKE) all +- cd streesrc; $(MAKE) all +- cd mm3src; $(MAKE) all ++ $(MAKE) -C libbasedir all ++ $(MAKE) -C streesrc all ++ $(MAKE) -C mm3src all + + clean: + rm -f *~ +@@ -10,11 +10,11 @@ clean: + cd mm3src; $(MAKE) clean + + mummer: +- cd libbasedir; $(MAKE) libbase.a +- cd streesrc; $(MAKE) libstree.a +- cd mm3src; $(MAKE) mummer ++ $(MAKE) -C libbasedir libbase.a ++ $(MAKE) -C streesrc libstree.a ++ $(MAKE) -C mm3src mummer + + splintall: +- cd libbasedir; ${MAKE} splintall +- cd streesrc; ${MAKE} splintall +- cd mm3src; ${MAKE} splintall ++ $(MAKE) -C libbasedir splintall ++ $(MAKE) -C streesrc splintall ++ $(MAKE) -C mm3src splintall diff --git a/sci-biology/mummer/files/mummer-3.20-gcc43.patch b/sci-biology/mummer/files/mummer-3.20-gcc43.patch new file mode 100644 index 000000000000..4d3edb41e46a --- /dev/null +++ b/sci-biology/mummer/files/mummer-3.20-gcc43.patch @@ -0,0 +1,12 @@ +--- src/tigr/show-diff.cc.orig 2008-06-16 17:55:34.000000000 +0000 ++++ src/tigr/show-diff.cc 2008-06-16 17:56:25.000000000 +0000 +@@ -14,6 +14,8 @@ + #include <cstdlib> + #include <cassert> + #include <climits> ++#include <algorithm> ++ + using namespace std; + + + |