Apply patches, fix bug 294738 and move binaries to libexec

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

5 files changed, 102 insertions, 9 deletions

diff --git a/sci-biology/vaal/ChangeLog b/sci-biology/vaal/ChangeLog
index bc23691ff3ec..d16a99ff8074 100644
--- a/sci-biology/vaal/ChangeLog
+++ b/sci-biology/vaal/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/vaal
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.3 2009/11/12 19:15:45 weaver Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.4 2010/02/14 19:50:10 weaver Exp $
+
+*vaal-1.2-r1 (14 Feb 2010)
+
+  14 Feb 2010; Andrey Kislyuk <weaver@gentoo.org>
+  +files/vaal-1.2-as-needed.patch, +files/vaal-1.2-respect-flags.patch,
+  -vaal-1.2.ebuild, +vaal-1.2-r1.ebuild:
+  Apply patches, fix bug 294738 and move binaries to libexec
 
   12 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> vaal-1.2.ebuild:
   Remove hardcoded version in SRC_URI
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
index 388ee464412e..b60c59372524 100644
--- a/sci-biology/vaal/Manifest
+++ b/sci-biology/vaal/Manifest
@@ -1,6 +1,8 @@
+AUX vaal-1.2-as-needed.patch 905 RMD160 5daf6a4603fb729bac33ad54cbf5a79be65860bd SHA1 ffae4e00b6cb0497e87cd09857c62ebe19449c79 SHA256 6d097b3b72d394753e194974acf98a347e7e7046aaf865949aa551f0ee08a1f2
 AUX vaal-1.2-gcc-x86-no-autocast.patch 1877 RMD160 dbcac734c896600c89c7c2ab73abeb03374a0bad SHA1 607371fad2443a65151b15ad6f08d4462056415b SHA256 a365d038dffdf6ea1ece2a0e55426c436f457b3cb0e640345decb00f2849a285
+AUX vaal-1.2-respect-flags.patch 1838 RMD160 fe1464f977dfd1abe34c736e19990eab5f413655 SHA1 a4b83b2896e3c92bba6182e173f204f374dcd433 SHA256 42a1435657533c39ef9011be722ee217d0823c0f5802aaf2365136fddae49866
 DIST VAAL.1.2.tgz 978333 RMD160 f81c1a33348e7c2ef2a6b07c1ceeeda564b9b521 SHA1 f51a4000149cbd9ae674ee0d7781c27aee6e31a9 SHA256 cfb9d73fd4ac5720f65b54e7f763e28a503d65c61269939d5f43dbf88dd17375
 DIST VAAL_manual.doc 48128 RMD160 08d809c847f1842483ed653df9bb6ed5ee1d10a8 SHA1 836f8be0f0200358131c23174eeca5d2d7454a68 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83
-EBUILD vaal-1.2.ebuild 1024 RMD160 22d3122bc94b10fe3fcd99518536844b285de362 SHA1 5a6d614b42403913f50153e10e3ae258d4e48c2a SHA256 583a194690a3837e6ccc495f34dc99f2cb8f713885132bc5198c9787c202f258
-MISC ChangeLog 598 RMD160 c4894d26bf9355a4b63863b47d2a5c25c8334d81 SHA1 70fd33584df7559d7a8eb16ace3e9ef78daba1db SHA256 f90b0d5b3e0d123b7f1891242ce9a992ada1e5f6951365ce72334a8c1e3a00d0
+EBUILD vaal-1.2-r1.ebuild 1097 RMD160 67eef005074040c7c9e0192147cbbeff02c865c4 SHA1 67e80bb076583cd173b87c0c5028fad4cad47e59 SHA256 ca425d9f49cc25f8837a058cc760ecf27a892fe7cb702ba53171ec333c69e75a
+MISC ChangeLog 851 RMD160 d94de44d7f7791483a15a9f78c53d857d2be0a6e SHA1 2dc2bf07bf013750e8e36f435080bffcb8058fc0 SHA256 4c6b2dc97cf9f2e3183de2a1c4d7de56e9b80c9d666e51fc83581456d20cf299
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/vaal/files/vaal-1.2-as-needed.patch b/sci-biology/vaal/files/vaal-1.2-as-needed.patch
new file mode 100644
index 000000000000..31649010dbe3
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-1.2-as-needed.patch
@@ -0,0 +1,22 @@
+--- VAAL.orig/MakeDepend.cc	2008-12-18 17:05:48.000000000 +0100
++++ VAAL/MakeDepend.cc	2010-02-14 13:42:23.734370178 +0100
+@@ -1195,9 +1195,6 @@
+       }
+     }
+     mf << " -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)"; 
+-    for ( set<string>::iterator dep_iter = lib_deps.begin(); 
+-	  dep_iter != lib_deps.end(); ++dep_iter )
+-      mf << " " << "$(" << *dep_iter << "_LFLAGS)";
+     for ( set<string>::iterator dep_iter = sharedlib_deps.begin();
+           dep_iter != sharedlib_deps.end(); ++dep_iter ) {
+       // Extract the symbolic name of this library from its filename.
+@@ -1208,6 +1205,9 @@
+       mf << " -l" << sharedlib_name;
+     }
+     mf << " -l" << libname;
++    for ( set<string>::iterator dep_iter = lib_deps.begin(); 
++	  dep_iter != lib_deps.end(); ++dep_iter )
++      mf << " " << "$(" << *dep_iter << "_LFLAGS)";
+     mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n";
+   }
+ }    
diff --git a/sci-biology/vaal/files/vaal-1.2-respect-flags.patch b/sci-biology/vaal/files/vaal-1.2-respect-flags.patch
new file mode 100644
index 000000000000..d3420556b608
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-1.2-respect-flags.patch
@@ -0,0 +1,60 @@
+--- VAAL.orig/Makefile.in	2009-04-02 21:43:42.000000000 +0200
++++ VAAL/Makefile.in	2010-02-14 14:20:26.222370302 +0100
+@@ -161,12 +161,16 @@
+ COMPILER	= @CC@
+ CPLUSPLUS	= @CXX@
+ 
++CFLAGS		= @CFLAGS@
++CXXFLAGS	= @CXXFLAGS@
++LDFLAGS 	= @LDFLAGS@
++
+ # QUIET=yes causes the compiler to be less verbose about warnings.
+ QUIET		= no
+ 
+ # DEBUG=yes forces out-of-date executables to be built with symbolic
+ # debugging information.  Any other value is ignored.
+-DEBUG		= yes
++DEBUG		= no
+ 
+ # OPTIM=<compiler optimization> forces user-defined optimizations to be used,
+ # rather than the compiler-specific default.  
+@@ -174,7 +178,7 @@
+ # If OPTIM=none, then no optimization is used.	
+ # If unset, defaults are used.
+ # -fno-exceptions
+-OPTIM		= 
++OPTIM		= none
+ 
+ # PROFILE=yes builds sampled-profiling (i.e. gprof) executables. Any other
+ # value is ignored.
+@@ -317,6 +321,7 @@
+ # Setup final compilation options:
+ 
+ CPP_OPTIONS	= \
++		$(CXXFLAGS) \
+ 		$(SYS_WARN) \
+ 		$(SYS_OPT) \
+ 		$(SYS_DEBUG) \
+@@ -328,6 +333,7 @@
+ 		@INCLUDES@
+ 
+ LINK_OPTIONS	= \
++		$(LDFLAGS) \
+ 		$(SYS_DEBUG) \
+ 		$(SYS_LINK) \
+ 		$(OMP_LINK) \
+@@ -406,12 +406,12 @@
+ 	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
+ 
+ checkLock: $(SRC)/util/checkLock.cc
+-	$(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock 
++	$(CPLUSPLUS) $(CXXFLAGS) $(SRC)/util/checkLock.cc $(LDFLAGS) -o $(BIN)/checkLock 
+ 
+ random/Random.o: random/Random.cc
+ 	@ mkdir -p $(OBJ)/${@D}
+ 	cp $(SRC)/random/Random.cc $(SRC)/random/Random.c
+-	$(CC) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o
++	$(CC) $(CFLAGS) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o
+ 	rm $(SRC)/random/Random.c
+ 
+ MemTracker.o: MemTracker.cc
diff --git a/sci-biology/vaal/vaal-1.2.ebuild b/sci-biology/vaal/vaal-1.2-r1.ebuild
index 58420917ef24..ead9c7a77f65 100644
--- a/sci-biology/vaal/vaal-1.2.ebuild
+++ b/sci-biology/vaal/vaal-1.2-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.2.ebuild,v 1.3 2009/11/12 19:15:45 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.2-r1.ebuild,v 1.1 2010/02/14 19:50:10 weaver Exp $
 
 EAPI="2"
 
@@ -21,16 +21,18 @@ RDEPEND="${DEPEND}"
 
 PATCHES=(
 	"${FILESDIR}"/${P}-gcc-x86-no-autocast.patch
+	"${FILESDIR}"/${P}-as-needed.patch
+	"${FILESDIR}"/${P}-respect-flags.patch
 )
 
 S="${WORKDIR}/VAAL"
 
 src_install() {
-	exeinto /usr/share/${PN}/bin
+	exeinto /usr/libexec/${PN}
 	doexe bin/* || die
-	echo "PATH=\"/usr/share/${PN}/bin\"" > "${S}/99${PN}"
+	echo "PATH=\"/usr/libexec/${PN}\"" > "${S}/99${PN}"
 	doenvd "${S}/99${PN}" || die
-	dosym /usr/share/${PN}/bin/VAALrun /usr/bin/VAALrun || die
+	dosym /usr/libexec/${PN}/VAALrun /usr/bin/VAALrun || die
 	insinto /usr/share/doc/${PF}
 	doins "${DISTDIR}/VAAL_manual.doc"
 }