path: root/sci-biology/blat/files/blat-34-fix-build-system.patch

--- a/blat/makefile
+++ b/blat/makefile
@@ -7,8 +7,7 @@
 O = blat.o
 
 blat: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
-	${STRIP} ${BINDIR}/blat${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
 
 all:
 	cd ../lib && ${MAKE}
--- a/gfClient/makefile
+++ b/gfClient/makefile
@@ -8,5 +8,4 @@
 X = gfClient
 
 gfClient: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
-	${STRIP} ${BINDIR}/$X${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
--- a/gfServer/makefile
+++ b/gfServer/makefile
@@ -8,8 +8,7 @@
 X = gfServer
 
 gfServer: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
-	${STRIP} ${BINDIR}/$X${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
 
 test:
 	${MKDIR} tests/output
--- a/hg/pslPretty/makefile
+++ b/hg/pslPretty/makefile
@@ -8,7 +8,7 @@
 O = pslPretty.o
 
 pslPretty: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
 
 test:: testRna testDnax
 
--- a/hg/pslReps/makefile
+++ b/hg/pslReps/makefile
@@ -9,7 +9,7 @@
 O = pslReps.o 
 
 pslReps: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
 
 lib:
 	cd ../../lib && ${MAKE}
--- a/hg/pslSort/makefile
+++ b/hg/pslSort/makefile
@@ -8,7 +8,7 @@
 O = pslSort.o
 
 pslSort: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
+	${CC} ${LDFLAGS} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
 
 
 lib:
--- a/inc/cgi_build_rules.mk
+++ b/inc/cgi_build_rules.mk
@@ -12,7 +12,6 @@
 	mv $A${EXE} ${CGI_BIN}-beta/$A
 
 strip::  compile
-	${STRIP} $A${EXE}
 	chmod g+w $A${EXE}
 	chmod a+rx $A${EXE}
 
--- 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:
@@ -36,9 +31,6 @@
     BINDIR = ${HOME}/bin/${MACHTYPE}
 endif
 MKDIR=mkdir -p
-ifeq (${STRIP},)
-   STRIP=strip
-endif
 CVS=cvs
 
 # portable naming of compiled executables: add ".exe" if compiled on 
@@ -55,6 +47,6 @@
 STRINGIFY = ${BINDIR}/stringify
 
 %.o: %.c
-	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
+	${CC} ${CPPFLAGS} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
 
 
--- a/jkOwnLib/makefile
+++ b/jkOwnLib/makefile
@@ -9,7 +9,7 @@
 T = ../lib/$(MACHTYPE)/jkOwnLib.a
 
 $(T): $(O) ../lib/$(MACHTYPE)
-	ar rcus $(T) $(O)
+	$(AR) rcus $(T) $(O)
 
 ../lib/$(MACHTYPE):
 	mkdir ../lib/$(MACHTYPE)
--- a/jkOwnLib/tests/freen/makefile
+++ b/jkOwnLib/tests/freen/makefile
@@ -7,5 +7,5 @@
 O = freen.o
 
 hello: freen.o
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L
 
--- a/lib/makefile
+++ b/lib/makefile
@@ -32,7 +32,7 @@
 
 
 $(MACHTYPE)/jkweb.a: $(O) $(MACHTYPE)
-	ar rcus $(MACHTYPE)/jkweb.a $(O)
+	$(AR) rcus $(MACHTYPE)/jkweb.a $(O)
 
 $(MACHTYPE):
 	mkdir $(MACHTYPE)
--- a/lib/tests/makefile
+++ b/lib/tests/makefile
@@ -14,22 +14,19 @@
 	${MKDIR} output ${BIN_DIR}
 
 errCatchTest: errCatchTest.o ${MYLIBS} mkdirs
-	${CC} ${COPT} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L
-	${STRIP} ${BIN_DIR}/errCatchTest${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L
 	${BIN_DIR}/errCatchTest secret > output/errCatch.good
 	diff expected/errCatch.good output/errCatch.good
 	${BIN_DIR}/errCatchTest bad > output/errCatch.bad
 	diff expected/errCatch.bad output/errCatch.bad
 
 htmlExpandUrlTest: htmlExpandUrlTest.o ${MYLIBS} mkdirs
-	${CC} ${COPT} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L
-	${STRIP} ${BIN_DIR}/htmlExpandUrlTest${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L
 	${BIN_DIR}/htmlExpandUrlTest > output/htmlExpandUrlTest 2>&1
 	diff expected/htmlExpandUrlTest output/htmlExpandUrlTest
 
 htmlPageTest: htmlPageTest.o ${MYLIBS} mkdirs
-	${CC} ${COPT} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L
-	${STRIP} ${BIN_DIR}/htmlPageTest${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L
 	${BIN_DIR}/htmlPageTest input/google.html > output/google.out
 	diff expected/google.out output/google.out
 
@@ -86,20 +83,20 @@
 	diff -b expected/$@.err output/$@.err
 
 ${BIN_DIR}/pipelineTester:  mkdirs pipelineTester.o ${MYLIBS}
-	${CC} ${COPT} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L
 
 
 dyStringTest: ${BIN_DIR}/dyStringTester mkdirs
 	${BIN_DIR}/dyStringTester
 
 ${BIN_DIR}/dyStringTester:  mkdirs dyStringTester.o ${MYLIBS}
-	${CC} ${COPT} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L
 
 
 mimeTests: mime1 mime2 mime3 mime4 mimeBin mime5 mimeAltHead mimeAutoBoundary mimeBlat
 
 ${BIN_DIR}/mimeTester:  mkdirs mimeTester.o ${MYLIBS}
-	${CC} ${COPT} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L
 
 
 mime1: ${BIN_DIR}/mimeTester mkdirs
@@ -142,7 +139,7 @@
 	${BIN_DIR}/mimeTester -sizeSeries=3000
 
 ${BIN_DIR}/htmlMimeTest:  mkdirs htmlMimeTest.o ${MYLIBS}
-	${CC} ${COPT} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L
 
 htmlMime1: ${BIN_DIR}/htmlMimeTest mkdirs
 	${BIN_DIR}/htmlMimeTest http://hgwdev.cse.ucsc.edu/cgi-bin/hgBlat input/htmlMime.txt 3490 3502 > output/$@.out
@@ -152,7 +149,7 @@
 base64Tests: base64Encode base64Decode
 
 ${BIN_DIR}/testBase64:  mkdirs testBase64.o ${MYLIBS}
-	${CC} ${COPT} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L
 
 base64Encode: ${BIN_DIR}/testBase64 mkdirs
 	${BIN_DIR}/testBase64 'My Test String' > output/$@.out
@@ -167,7 +164,7 @@
 quotedPTests: quotedPEncode quotedPDecode
 
 ${BIN_DIR}/testQuotedP:  mkdirs testQuotedP.o ${MYLIBS}
-	${CC} ${COPT} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L
 
 quotedPEncode: ${BIN_DIR}/testQuotedP mkdirs
 	${BIN_DIR}/testQuotedP 'taxes are quite high ' > output/$@.out
@@ -178,14 +175,14 @@
 	diff expected/$@.out output/$@.out
 
 ${BIN_DIR}/mimeDecodeTest:  mkdirs mimeDecodeTest.o ${MYLIBS}
-	${CC} ${COPT} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L
 
 mimeDecodeTest: ${BIN_DIR}/mimeDecodeTest mkdirs
 	${BIN_DIR}/mimeDecodeTest -cid -autoBoundary output < input/$@.txt
 	diff expected/noName1.html output/noName1.html
 
 ${BIN_DIR}/safeTester:  mkdirs safeTester.o ${MYLIBS}
-	${CC} ${COPT} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L
 
 safeTest: ${BIN_DIR}/safeTester mkdirs
 	${BIN_DIR}/safeTester
--- 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
--- a/utils/faToNib/makefile
+++ b/utils/faToNib/makefile
@@ -8,4 +8,4 @@
 O = faToNib.o
 
 faToNib: $O $(MYLIBS)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
--- a/utils/faToTwoBit/makefile
+++ b/utils/faToTwoBit/makefile
@@ -7,8 +7,7 @@
 O = faToTwoBit.o
 
 faToTwoBit: $O ${MYLIBS}
-	${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
-	${STRIP} ${BINDIR}/faToTwoBit${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
 
 clean:
 	rm -f $O
--- a/utils/nibFrag/makefile
+++ b/utils/nibFrag/makefile
@@ -4,7 +4,7 @@
 O = nibFrag.o 
 
 nibFrag: $(O)
-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
 
 
 
--- a/utils/twoBitInfo/makefile
+++ b/utils/twoBitInfo/makefile
@@ -7,8 +7,7 @@
 O = twoBitInfo.o
 
 twoBitInfo: $O ${MYLIBS}
-	${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
-	${STRIP} ${BINDIR}/twoBitInfo${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
 
 clean:
 	rm -f $O
--- a/utils/twoBitToFa/makefile
+++ b/utils/twoBitToFa/makefile
@@ -8,8 +8,7 @@
 O = twoBitToFa.o
 
 twoBitToFa: $O ${MYLIBS}
-	${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
-	#${STRIP} ${BINDIR}/twoBitToFa${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
 
 clean:
 	rm -f $O
--- a/webBlat/makefile
+++ b/webBlat/makefile
@@ -7,8 +7,7 @@
 O = webBlat.o
 
 webBlat: $O ${MYLIBS}
-	${CC} ${COPT} -o webBlat $O ${MYLIBS} $L
-	${STRIP} webBlat${EXE}
+	${CC} ${LDFLAGS} ${CFLAGS} -o webBlat $O ${MYLIBS} $L
 
 installOsX: webBlat
 	cp webBlat /Library/WebServer/CGI-Executables