Fixed unresolved symbols with as-needed (see bug #207304).

Package-Manager: portage-2.1.4

5 files changed, 67 insertions, 19 deletions

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index d1e75ae470f0..1de7d18f5144 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/emboss
-# Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.45 2007/07/22 07:32:37 dberkholz Exp $
+# Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.46 2008/01/25 23:51:41 markusle Exp $
+
+  25 Jan 2008; Markus Dittrich <markusle@gentoo.org>
+  +files/emboss-5.0.0-as-needed.patch, emboss-4.0.0.ebuild,
+  emboss-5.0.0.ebuild:
+  Fixed unresolved symbols with as-needed (see bug #207304).
 
   22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; emboss-4.0.0.ebuild:
   Drop virtual/x11 references.
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index c206f0ab243f..1440566df274 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -6,24 +6,28 @@ AUX README.Gentoo 1326 RMD160 bfaa4d7d1218d3bd4ea58d54d000da7f58b6bca6 SHA1 8cf1
 MD5 615888722f8d6a0c918f936e0cc1cfcd files/README.Gentoo 1326
 RMD160 bfaa4d7d1218d3bd4ea58d54d000da7f58b6bca6 files/README.Gentoo 1326
 SHA256 33b517b977cc85824847bd6cf4113489a5554fb014f1a6b1d22d6f80c3487e9f files/README.Gentoo 1326
+AUX emboss-5.0.0-as-needed.patch 1751 RMD160 f43faab31a3d5afb4b73704ba597de578668ae48 SHA1 a108e5f68af9c14363bc56c849c9143fcb7675ba SHA256 e57a60d911e32f1aea16c079e2fd0910a5f7ed43752ea71094d3f3b7575617d3
+MD5 9fdd03308234a9284b8ffbf97f4d84d7 files/emboss-5.0.0-as-needed.patch 1751
+RMD160 f43faab31a3d5afb4b73704ba597de578668ae48 files/emboss-5.0.0-as-needed.patch 1751
+SHA256 e57a60d911e32f1aea16c079e2fd0910a5f7ed43752ea71094d3f3b7575617d3 files/emboss-5.0.0-as-needed.patch 1751
 AUX emboss-README.Gentoo-1 1474 RMD160 a116b4516cd0d8e0b28734bf1e51f1e0833737c4 SHA1 ec23610137ebddc3fc15976757d2cdebd741f9ec SHA256 e97558bbc8296f2e9395080061e494b282303ed69e1d6eb45554846617b47abd
 MD5 f625f2d9c5bdbdc6799947f73c93da7c files/emboss-README.Gentoo-1 1474
 RMD160 a116b4516cd0d8e0b28734bf1e51f1e0833737c4 files/emboss-README.Gentoo-1 1474
 SHA256 e97558bbc8296f2e9395080061e494b282303ed69e1d6eb45554846617b47abd files/emboss-README.Gentoo-1 1474
 DIST EMBOSS-4.0.0.tar.gz 17651607 RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 SHA1 784c729f2d2e746339a90048277c9e4f052e036a SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231
 DIST EMBOSS-5.0.0.tar.gz 20666560 RMD160 1bf510c0919d991e4ba67182137448dee49bab4d SHA1 1ad4edc4808a8225fe8d574e8a7d0686be99cac6 SHA256 64e6f09b82a719ff26de7f21fdf7d2bd605d2c664384c1c7b48f9d245d5f40ae
-EBUILD emboss-4.0.0.ebuild 2983 RMD160 dfb77317efe47d70b09f648d0cbdb2befc5e6095 SHA1 749048723387405379f5e37581f849d57d291ed6 SHA256 6ece689be9b9ed839fae1697106e2cbd1abda2ab3536533dc55714e6db2dfbc9
-MD5 709fbec93234aba3a210610eb840e680 emboss-4.0.0.ebuild 2983
-RMD160 dfb77317efe47d70b09f648d0cbdb2befc5e6095 emboss-4.0.0.ebuild 2983
-SHA256 6ece689be9b9ed839fae1697106e2cbd1abda2ab3536533dc55714e6db2dfbc9 emboss-4.0.0.ebuild 2983
-EBUILD emboss-5.0.0.ebuild 3143 RMD160 765d21355731a6a790afd9e280e048998915190f SHA1 5233be4d5edd5043ebe7fb6da15fda2d0f638ccd SHA256 48055bdca89cc1add72998e251c4bb6904e7f2ee44237c13fc1af1fb85387d6e
-MD5 f9201389e5075f12b859da8b327992d4 emboss-5.0.0.ebuild 3143
-RMD160 765d21355731a6a790afd9e280e048998915190f emboss-5.0.0.ebuild 3143
-SHA256 48055bdca89cc1add72998e251c4bb6904e7f2ee44237c13fc1af1fb85387d6e emboss-5.0.0.ebuild 3143
-MISC ChangeLog 8057 RMD160 f0972ec038deb39ff064961399061e6e552115cd SHA1 420b78f16933cc57fe4cc3570fdde4fdd9f68dff SHA256 c7439c11a74666a68c7b90a8935fbf58a5a5436117850fa33686185ca5dcb5b7
-MD5 d9b5419fcd9618d7b3bffb52da96ea36 ChangeLog 8057
-RMD160 f0972ec038deb39ff064961399061e6e552115cd ChangeLog 8057
-SHA256 c7439c11a74666a68c7b90a8935fbf58a5a5436117850fa33686185ca5dcb5b7 ChangeLog 8057
+EBUILD emboss-4.0.0.ebuild 2985 RMD160 f97e44ba4e85b434862934d5f41b95c9148bb144 SHA1 1739fee6a460fb0e0e48150e5aac266d4fbcce8e SHA256 9465b53eb6ccc94ddfaee9e664d3bf705a529d64fcfbca0084e0cd37ce22c27c
+MD5 581b734e7316e20ffdb70433a20cb93b emboss-4.0.0.ebuild 2985
+RMD160 f97e44ba4e85b434862934d5f41b95c9148bb144 emboss-4.0.0.ebuild 2985
+SHA256 9465b53eb6ccc94ddfaee9e664d3bf705a529d64fcfbca0084e0cd37ce22c27c emboss-4.0.0.ebuild 2985
+EBUILD emboss-5.0.0.ebuild 3443 RMD160 e79a1e380c004634334b63edc1fd79d1ce23c44e SHA1 40e92f01e78e26905de61b9fbbd67400746aaa7a SHA256 4b05e9d49104a0e6f1d597ac3d5b69ff52fd85e742bfe206312f5333740f0006
+MD5 0f5972742f1b908215b5cecd040c6c1d emboss-5.0.0.ebuild 3443
+RMD160 e79a1e380c004634334b63edc1fd79d1ce23c44e emboss-5.0.0.ebuild 3443
+SHA256 4b05e9d49104a0e6f1d597ac3d5b69ff52fd85e742bfe206312f5333740f0006 emboss-5.0.0.ebuild 3443
+MISC ChangeLog 8254 RMD160 611978a6833d58763782335e8d228679935f220d SHA1 36c9344393e75f74cd16905be159ac8789fdde98 SHA256 03e8122b40bd8935ad6f00ed12e0e3edba8465815d4a5ca1180f14117cdc8a72
+MD5 a6e4531d60d804e7a571404619628fe7 ChangeLog 8254
+RMD160 611978a6833d58763782335e8d228679935f220d ChangeLog 8254
+SHA256 03e8122b40bd8935ad6f00ed12e0e3edba8465815d4a5ca1180f14117cdc8a72 ChangeLog 8254
 MISC metadata.xml 1021 RMD160 ee767f436af5f815ecb9526df9063438dab8eb14 SHA1 eff46db435f88e0b457ce2a38e5ff786ae6324e1 SHA256 0c5af548d0483d41a3344695cb04acaf0974fb56b70bc1e2ec0a9749ecbc45a0
 MD5 ecba11e4d50ee5cc740817f5becffa83 metadata.xml 1021
 RMD160 ee767f436af5f815ecb9526df9063438dab8eb14 metadata.xml 1021
diff --git a/sci-biology/emboss/emboss-4.0.0.ebuild b/sci-biology/emboss/emboss-4.0.0.ebuild
index 8d03a59bf2b2..0ced2e60f033 100644
--- a/sci-biology/emboss/emboss-4.0.0.ebuild
+++ b/sci-biology/emboss/emboss-4.0.0.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2007 Gentoo Foundation
+# Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-4.0.0.ebuild,v 1.9 2007/07/22 07:32:37 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-4.0.0.ebuild,v 1.10 2008/01/25 23:51:41 markusle Exp $
 
 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
 HOMEPAGE="http://emboss.sourceforge.net/"
@@ -54,7 +54,7 @@ src_install() {
 			|| die "Failed to install documentation."
 
 	# Install env file for setting libplplot and acd files path.
-	doenvd ${FILESDIR}/22emboss || die "Failed to install environment file."
+	doenvd "${FILESDIR}"/22emboss || die "Failed to install environment file."
 
 	# Symlink preinstalled docs to /usr/share/doc.
 	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
diff --git a/sci-biology/emboss/emboss-5.0.0.ebuild b/sci-biology/emboss/emboss-5.0.0.ebuild
index 5d7a83176305..7dc99b1a7050 100644
--- a/sci-biology/emboss/emboss-5.0.0.ebuild
+++ b/sci-biology/emboss/emboss-5.0.0.ebuild
@@ -1,6 +1,8 @@
-# Copyright 1999-2007 Gentoo Foundation
+# Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-5.0.0.ebuild,v 1.1 2007/07/18 00:55:33 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-5.0.0.ebuild,v 1.2 2008/01/25 23:51:41 markusle Exp $
+
+inherit eutils
 
 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
 HOMEPAGE="http://emboss.sourceforge.net/"
@@ -33,6 +35,19 @@ PDEPEND="!minimal? (
 
 S="${WORKDIR}/EMBOSS-${PV}"
 
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-as-needed.patch
+
+	local link_string="-lX11";
+	if use png; then
+		link_string="${link_string} -lgd -lpng"
+	fi
+	sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
+		|| die "Failed to patch ajax Makefile"
+}
+
 src_compile() {
 	EXTRA_CONF="--includedir=${D}/usr/include/emboss"
 	! use X && EXTRA_CONF="${EXTRA_CONF} --without-x"
diff --git a/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch b/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch
new file mode 100644
index 000000000000..9915f95376d0
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch
@@ -0,0 +1,24 @@
+diff -Naur EMBOSS-5.0.0.old/ajax/Makefile.in EMBOSS-5.0.0/ajax/Makefile.in
+--- EMBOSS-5.0.0.old/ajax/Makefile.in	2007-07-12 05:53:32.000000000 -0500
++++ EMBOSS-5.0.0/ajax/Makefile.in	2008-01-25 16:43:51.000000000 -0500
+@@ -244,7 +244,7 @@
+ top_srcdir = @top_srcdir@
+ @ISCYGWIN_FALSE@lib_LTLIBRARIES = libajax.la libajaxg.la
+ @ISCYGWIN_TRUE@lib_LTLIBRARIES = libajax.la
+-@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = 
++@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = -lm -L../plplot/.libs -leplplot
+ @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm
+ @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm
+ @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot
+diff -Naur EMBOSS-5.0.0.old/plplot/Makefile.in EMBOSS-5.0.0/plplot/Makefile.in
+--- EMBOSS-5.0.0.old/plplot/Makefile.in	2007-07-12 05:53:36.000000000 -0500
++++ EMBOSS-5.0.0/plplot/Makefile.in	2008-01-25 16:42:51.000000000 -0500
+@@ -229,7 +229,7 @@
+ lib_LTLIBRARIES = libeplplot.la
+ @AMPNG_FALSE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lX11
+ @AMPNG_TRUE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lgd -lpng -lz -lX11 -lm
+-@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = 
++@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = PATCH_PLPLOT
+ @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -lX11 -lgd -lpng -lz
+ INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\"
+ PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \