sci-biology/blat/files/34-gentoo.patch

 blat/makefile             |    2 +-
 gfClient/makefile         |    2 +-
 gfServer/makefile         |    2 +-
 hg/pslPretty/makefile     |    2 +-
 hg/pslReps/makefile       |    2 +-
 hg/pslSort/makefile       |    2 +-
 inc/common.mk             |   11 +++--------
 makefile                  |   28 ++++++++++++++--------------
 utils/faToNib/makefile    |    2 +-
 utils/faToTwoBit/makefile |    2 +-
 utils/nibFrag/makefile    |    2 +-
 utils/twoBitInfo/makefile |    2 +-
 utils/twoBitToFa/makefile |    2 +-
 13 files changed, 28 insertions(+), 33 deletions(-)

diff --git a/blat/makefile b/blat/makefile
index b889c7b..739503a 100644
--- a/blat/makefile
+++ b/blat/makefile
@@ -7,7 +7,7 @@ MYLIBS =  $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a
 O = blat.o
 
 blat: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
 	${STRIP} ${BINDIR}/blat${EXE}
 
 all:
diff --git a/gfClient/makefile b/gfClient/makefile
index c3288de..36e957e 100644
--- a/gfClient/makefile
+++ b/gfClient/makefile
@@ -8,5 +8,5 @@ O = gfClient.o
 X = gfClient
 
 gfClient: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
 	${STRIP} ${BINDIR}/$X${EXE}
diff --git a/gfServer/makefile b/gfServer/makefile
index c06b3a5..f042d22 100644
--- a/gfServer/makefile
+++ b/gfServer/makefile
@@ -8,7 +8,7 @@ O = gfServer.o
 X = gfServer
 
 gfServer: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
 	${STRIP} ${BINDIR}/$X${EXE}
 
 test:
diff --git a/hg/pslPretty/makefile b/hg/pslPretty/makefile
index c780b96..cbbcd0d 100644
--- a/hg/pslPretty/makefile
+++ b/hg/pslPretty/makefile
@@ -8,7 +8,7 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
 O = pslPretty.o
 
 pslPretty: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
 
 test:: testRna testDnax
 
diff --git a/hg/pslReps/makefile b/hg/pslReps/makefile
index 6e8f6d7..2b73b60 100644
--- a/hg/pslReps/makefile
+++ b/hg/pslReps/makefile
@@ -9,7 +9,7 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
 O = pslReps.o 
 
 pslReps: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
 
 lib:
 	cd ../../lib && ${MAKE}
diff --git a/hg/pslSort/makefile b/hg/pslSort/makefile
index 81fe083..eb63257 100644
--- a/hg/pslSort/makefile
+++ b/hg/pslSort/makefile
@@ -8,7 +8,7 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
 O = pslSort.o
 
 pslSort: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
 
 
 lib:
diff --git a/inc/common.mk b/inc/common.mk
index 1823163..3a04e2b 100644
--- a/inc/common.mk
+++ b/inc/common.mk
@@ -1,20 +1,15 @@
-CC=gcc
-ifeq (${COPT},)
-    COPT=-O
-endif
-CFLAGS=
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
 HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc
 
 # Stronger warning checks, and warnings-->errors, for libraries and CGIs:
 ifeq (darwin,$(findstring darwin,${OSTYPE}))
-    HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable
+    HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable
 else
   ifeq (solaris,$(findstring solaris,${OSTYPE}))
     HG_WARN_ERR = -DJK_WARN -Wall
   else
-    HG_WARN_ERR = -DJK_WARN -Wall -Werror
+    HG_WARN_ERR = -DJK_WARN -Wall
   endif
 endif
 # Apply the stronger checks to all code on our development machine:
@@ -37,7 +32,7 @@ ifeq (${BINDIR},)
 endif
 MKDIR=mkdir -p
 ifeq (${STRIP},)
-   STRIP=strip
+   STRIP=true
 endif
 CVS=cvs
 
diff --git a/makefile b/makefile
index 6f9fddf..dded1cd 100644
--- a/makefile
+++ b/makefile
@@ -1,18 +1,18 @@
 all:
-	cd lib && ${MAKE}
-	cd jkOwnLib && ${MAKE}
-	cd blat && $(MAKE)
-	cd gfClient && $(MAKE)
-	cd gfServer && $(MAKE)
-	cd hg/pslPretty && $(MAKE)
-	cd hg/pslReps && $(MAKE)
-	cd hg/pslSort && $(MAKE)
-	cd utils/nibFrag && $(MAKE)
-	cd utils/faToNib && $(MAKE)
-	cd utils/faToTwoBit && $(MAKE)
-	cd utils/twoBitToFa && $(MAKE)
-	cd utils/twoBitInfo && $(MAKE)
-	cd webBlat && $(MAKE)
+	$(MAKE) -C lib
+	$(MAKE) -C jkOwnLib
+	$(MAKE) -C blat
+	$(MAKE) -C gfClient
+	$(MAKE) -C gfServer
+	$(MAKE) -C hg/pslPretty
+	$(MAKE) -C hg/pslReps
+	$(MAKE) -C hg/pslSort
+	$(MAKE) -C utils/nibFrag
+	$(MAKE) -C utils/faToNib
+	$(MAKE) -C utils/faToTwoBit
+	$(MAKE) -C utils/twoBitToFa
+	$(MAKE) -C utils/twoBitInfo
+	$(MAKE) -C webBlat
 
 clean:
 	rm -f */*.o */*/*.o
diff --git a/utils/faToNib/makefile b/utils/faToNib/makefile
index fd0e3eb..63a1593 100644
--- a/utils/faToNib/makefile
+++ b/utils/faToNib/makefile
@@ -8,4 +8,4 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
 O = faToNib.o
 
 faToNib: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
diff --git a/utils/faToTwoBit/makefile b/utils/faToTwoBit/makefile
index b1b44a9..1e8c1c8 100644
--- a/utils/faToTwoBit/makefile
+++ b/utils/faToTwoBit/makefile
@@ -7,7 +7,7 @@ MYLIBS =  ${MYLIBDIR}/jkweb.a
 O = faToTwoBit.o
 
 faToTwoBit: $O ${MYLIBS}
-	${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
+	${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
 	${STRIP} ${BINDIR}/faToTwoBit${EXE}
 
 clean:
diff --git a/utils/nibFrag/makefile b/utils/nibFrag/makefile
index 260a6f3..e37b9ab 100755
--- a/utils/nibFrag/makefile
+++ b/utils/nibFrag/makefile
@@ -4,7 +4,7 @@ include ../../inc/common.mk
 O = nibFrag.o 
 
 nibFrag: $(O)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
 
 
 
diff --git a/utils/twoBitInfo/makefile b/utils/twoBitInfo/makefile
index 649784f..9434d1c 100644
--- a/utils/twoBitInfo/makefile
+++ b/utils/twoBitInfo/makefile
@@ -7,7 +7,7 @@ MYLIBS =  ${MYLIBDIR}/jkweb.a
 O = twoBitInfo.o
 
 twoBitInfo: $O ${MYLIBS}
-	${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
+	${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
 	${STRIP} ${BINDIR}/twoBitInfo${EXE}
 
 clean:
diff --git a/utils/twoBitToFa/makefile b/utils/twoBitToFa/makefile
index cf979f2..081f3b8 100644
--- a/utils/twoBitToFa/makefile
+++ b/utils/twoBitToFa/makefile
@@ -8,7 +8,7 @@ MYLIBS =  ${MYLIBDIR}/jkweb.a
 O = twoBitToFa.o
 
 twoBitToFa: $O ${MYLIBS}
-	${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
+	${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
 	#${STRIP} ${BINDIR}/twoBitToFa${EXE}
 
 clean: