From a711502749e9950778bece5ed06709d7cb0dbaca Mon Sep 17 00:00:00 2001 From: Markus Dittrich Date: Fri, 25 Jan 2008 23:51:42 +0000 Subject: Fixed unresolved symbols with as-needed (see bug #207304). Package-Manager: portage-2.1.4 --- sci-biology/emboss/ChangeLog | 9 +++++-- sci-biology/emboss/Manifest | 28 ++++++++++++---------- sci-biology/emboss/emboss-4.0.0.ebuild | 6 ++--- sci-biology/emboss/emboss-5.0.0.ebuild | 19 +++++++++++++-- .../emboss/files/emboss-5.0.0-as-needed.patch | 24 +++++++++++++++++++ 5 files changed, 67 insertions(+), 19 deletions(-) create mode 100644 sci-biology/emboss/files/emboss-5.0.0-as-needed.patch (limited to 'sci-biology') 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 + +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 ; 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 \ -- cgit v1.2.3-65-gdbad