Respect LDFLAGS, #337438

Package-Manager: portage-2.2.0_alpha41/cvs/Linux x86_64

4 files changed, 286 insertions, 7 deletions

diff --git a/sci-biology/blat/ChangeLog b/sci-biology/blat/ChangeLog
index 5f894e61f1f9..e467517affc7 100644
--- a/sci-biology/blat/ChangeLog
+++ b/sci-biology/blat/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/blat
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/blat/ChangeLog,v 1.2 2009/03/22 16:35:06 maekke Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/blat/ChangeLog,v 1.3 2011/06/20 07:59:53 jlec Exp $
+
+*blat-34-r1 (20 Jun 2011)
+
+  20 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/34-gentoo.patch,
+  +blat-34-r1.ebuild:
+  Respect LDFLAGS, #337438
 
   22 Mar 2009; Markus Meier <maekke@gentoo.org> blat-34.ebuild:
   amd64/x86 stable, bug #263045
diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest
index 43b5841dccb0..16adc7d682f9 100644
--- a/sci-biology/blat/Manifest
+++ b/sci-biology/blat/Manifest
@@ -1,14 +1,16 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
+AUX 34-gentoo.patch 6828 RMD160 e87cfb5e21312bc7aff45cdaec8596e0045ace0e SHA1 fc872a136085e3b9ce6a11c92ff2cd964db80bf1 SHA256 bc26df63c41e5fb816669a7d8c03cf8c9484799360ea3b4b88763ab165ad1719
 DIST blatSrc34.zip 2142975 RMD160 6c8226305c56ea56504103db6ef401841bc0c6f7 SHA1 4208451b5fa5f6cf30d15afb1df79edc850735db SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
+EBUILD blat-34-r1.ebuild 1040 RMD160 30c7983dec2353d3b34b1a213b7777e2556fe0ad SHA1 8163955ccc0ba71dc806cfe148294de3bec89acf SHA256 de2a89d529d87b107c1dab6dab1800121d0874c924ba4ee2811be574d09b6e8b
 EBUILD blat-34.ebuild 986 RMD160 8c3e1becc2df0e8272a33ac55a2276038a996c4e SHA1 b3a2aef777e6b07e10f4fb7dc7d3873663cc782d SHA256 030a736e1ed5af3ef908b6aa7cade56ca91ae4cf6e278e25d65e1d85bf3c3c87
-MISC ChangeLog 441 RMD160 aa6b7d010df45be4162105c18bccb8f5919a51f3 SHA1 366b46db4cd8e983fbd0f5a3a7b5a7dfece43943 SHA256 6b05f2f1397801d7860bbf4aa9a94d90fe816640d4efd50c35101a0c46b62446
+MISC ChangeLog 587 RMD160 41ac42cc404b3fb67ffcee491cba85d4a3d74d98 SHA1 bfd552a1ddb11b7b97ea15bd8f859576f6442136 SHA256 3f40d9977dfcfbc90a1e718f139d09f0a7d362f2e4ada3ed90ab0997c251c9d7
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.9 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAknGaMgACgkQkKaRLQcq0GI1TgCfbijXAdWil2qMSLqQEB9fKfDU
-yyAAoJojPLcGXxJBQODQj+EAgR10Ino4
-=2Rgi
+iEYEARECAAYFAk3+/f8ACgkQgAnW8HDreRYsTwCgi/lHLnD/iVITQbCKQnnUiqt0
+owgAoM0pgn9GGTNfTODcBeFNFtmbEUY/
+=Wv60
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/blat/blat-34-r1.ebuild b/sci-biology/blat/blat-34-r1.ebuild
new file mode 100644
index 000000000000..0fa39a82282d
--- /dev/null
+++ b/sci-biology/blat/blat-34-r1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/blat/blat-34-r1.ebuild,v 1.1 2011/06/20 07:59:53 jlec Exp $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+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}${PV}.zip"
+
+SLOT="0"
+LICENSE="blat"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S="${WORKDIR}/${MY_PN}"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+	sed \
+		-e "1i\CFLAGS=${CFLAGS}" \
+		-e "1i\LDFLAGS=${LDFLAGS}" \
+		-i inc/common.mk || die
+	tc-export CC
+}
+
+src_compile() {
+	MACHTYPE=$(tc-arch)
+	[[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
+	mkdir -p "${S}/bin/${MACHTYPE}"
+	emake MACHTYPE="${MACHTYPE}" HOME="${S}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	MACHTYPE=$(tc-arch)
+	[[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
+	dobin "${S}/bin/${MACHTYPE}/"*
+}
diff --git a/sci-biology/blat/files/34-gentoo.patch b/sci-biology/blat/files/34-gentoo.patch
new file mode 100644
index 000000000000..8bdd05bff68d
--- /dev/null
+++ b/sci-biology/blat/files/34-gentoo.patch
@@ -0,0 +1,226 @@
+ 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: