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author | David Seifert <soap@gentoo.org> | 2022-07-07 21:56:45 +0200 |
---|---|---|
committer | David Seifert <soap@gentoo.org> | 2022-07-07 21:56:45 +0200 |
commit | 047c13024df906142571f092249bd6f181c13b07 (patch) | |
tree | 831f42ffd25a6a62d1a093ea59c38b24c71e0841 | |
parent | sci-biology/biosql: update EAPI 6 -> 8 (diff) | |
download | gentoo-047c13024df906142571f092249bd6f181c13b07.tar.gz gentoo-047c13024df906142571f092249bd6f181c13b07.tar.bz2 gentoo-047c13024df906142571f092249bd6f181c13b07.zip |
sci-biology/blat: update EAPI 6 -> 8
Closes: https://bugs.gentoo.org/730780
Closes: https://bugs.gentoo.org/730782
Closes: https://bugs.gentoo.org/731744
Signed-off-by: David Seifert <soap@gentoo.org>
-rw-r--r-- | sci-biology/blat/blat-34-r3.ebuild (renamed from sci-biology/blat/blat-34-r2.ebuild) | 13 | ||||
-rw-r--r-- | sci-biology/blat/files/blat-34-fix-build-system.patch | 195 |
2 files changed, 173 insertions, 35 deletions
diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r3.ebuild index 7c7004cf950e..18c4128ec578 100644 --- a/sci-biology/blat/blat-34-r2.ebuild +++ b/sci-biology/blat/blat-34-r3.ebuild @@ -1,25 +1,22 @@ -# Copyright 2022 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs -MY_PN=${PN}Src +MY_PN="${PN}Src" DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" HOMEPAGE="http://www.cse.ucsc.edu/~kent/" SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" +S="${WORKDIR}/${MY_PN}" LICENSE="blat" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" -RDEPEND="" -DEPEND="app-arch/unzip" - -S=${WORKDIR}/${MY_PN} +BDEPEND="app-arch/unzip" PATCHES=( "${FILESDIR}"/${PN}-34-fix-build-system.patch diff --git a/sci-biology/blat/files/blat-34-fix-build-system.patch b/sci-biology/blat/files/blat-34-fix-build-system.patch index 361149cc1211..9aca3f841315 100644 --- a/sci-biology/blat/files/blat-34-fix-build-system.patch +++ b/sci-biology/blat/files/blat-34-fix-build-system.patch @@ -1,34 +1,36 @@ --- a/blat/makefile +++ b/blat/makefile -@@ -7,7 +7,7 @@ +@@ -7,8 +7,7 @@ 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} +- ${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 +8,5 @@ +@@ -8,5 +8,4 @@ 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} +- ${STRIP} ${BINDIR}/$X${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L --- a/gfServer/makefile +++ b/gfServer/makefile -@@ -8,7 +8,7 @@ +@@ -8,8 +8,7 @@ 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} +- ${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 @@ @@ -36,7 +38,7 @@ pslPretty: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L test:: testRna testDnax @@ -47,7 +49,7 @@ pslReps: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L lib: cd ../../lib && ${MAKE} @@ -58,10 +60,20 @@ pslSort: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -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 @@ @@ -87,15 +99,24 @@ endif endif # Apply the stronger checks to all code on our development machine: -@@ -37,7 +32,7 @@ +@@ -36,9 +31,6 @@ + BINDIR = ${HOME}/bin/${MACHTYPE} endif MKDIR=mkdir -p - ifeq (${STRIP},) +-ifeq (${STRIP},) - STRIP=strip -+ STRIP=true - endif +-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 $< + + --- a/jkOwnLib/makefile +++ b/jkOwnLib/makefile @@ -9,7 +9,7 @@ @@ -107,6 +128,15 @@ ../lib/$(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 @@ @@ -118,6 +148,102 @@ $(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 @@ @@ -160,18 +286,19 @@ faToNib: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L --- a/utils/faToTwoBit/makefile +++ b/utils/faToTwoBit/makefile -@@ -7,7 +7,7 @@ +@@ -7,8 +7,7 @@ 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} +- ${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 @@ @@ -179,29 +306,43 @@ 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 ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a --- a/utils/twoBitInfo/makefile +++ b/utils/twoBitInfo/makefile -@@ -7,7 +7,7 @@ +@@ -7,8 +7,7 @@ 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} +- ${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 -@@ -8,7 +8,7 @@ +@@ -8,8 +8,7 @@ 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} +- #${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 |