diff options
| -rw-r--r-- | sci-chemistry/pdb2pqr/ChangeLog | 7 | ||||
| -rw-r--r-- | sci-chemistry/pdb2pqr/Manifest | 6 | ||||
| -rw-r--r-- | sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch | 24 | ||||
| -rw-r--r-- | sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild | 6 |
4 files changed, 27 insertions, 16 deletions
diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog index 7bc7aa0be186..fb5b45682d24 100644 --- a/sci-chemistry/pdb2pqr/ChangeLog +++ b/sci-chemistry/pdb2pqr/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/pdb2pqr # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.17 2009/05/24 07:50:41 je_fro Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.18 2009/09/24 23:43:11 markusle Exp $ + + 24 Sep 2009; Markus Dittrich <markusle@gentoo.org> + pdb2pqr-1.4.0-r1.ebuild, files/pdb2pqr-1.4.0-automagic.patch: + Fixed automagic patch to honor --without-opal (fixes bug #278199). + Thanks much to Kacper Kowalik for his patch. *pdb2pqr-1.4.0-r1 (24 May 2009) diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest index 43ce9714564c..509764427807 100644 --- a/sci-chemistry/pdb2pqr/Manifest +++ b/sci-chemistry/pdb2pqr/Manifest @@ -2,7 +2,7 @@ AUX pdb2pqr-1.1.2-fpic-gentoo.patch 668 RMD160 e076ebcfe1e0fd39ca7b2219b6d9938b6 AUX pdb2pqr-1.1.2-gcc4-gentoo.patch 1104 RMD160 87d7c92e4f24be4f205379acafdc9c41b8e99a9b SHA1 346ed354808f2d902a2d4076e9c41690a83995f5 SHA256 164ae1a21de69ea97f5439a15004d1441fc7d11cbd79cf1c5ab777363b1e3019 AUX pdb2pqr-1.3.0-gcc4.3.patch 349 RMD160 a7e241b288738faaee678609c61968dba990b9a3 SHA1 95e0dcb30e926f0bab2068bff550427a1a3a623e SHA256 4e65916b3370bc3c4690ca9424629a928f9753879939f0ebb881304331fab946 AUX pdb2pqr-1.3.0-ldflags.patch 803 RMD160 ecc52d97bae89e1a961531eb5e4c87d456e87919 SHA1 ba777c53835045fd4538f3e1104a18d12df8d935 SHA256 8d2cf1f0d206e4162193877dd577ff0835f8e390d779ddfa4b73d30734dede77 -AUX pdb2pqr-1.4.0-automagic.patch 2962 RMD160 aa3dbdde3174c3035b8bea7a8ceb79733fc1a175 SHA1 22da361d832f9260d3cec1468535e28647357b6d SHA256 1a2dbd1b75be1b578d424506a6ff0365d2105bf57d36afe6a91751482da1b9bf +AUX pdb2pqr-1.4.0-automagic.patch 3526 RMD160 c4d662e68352d93f913fdc83b5c733a555a9bc17 SHA1 64598bff69e627a27ffa550ad5f3b38898a3a9cf SHA256 f145bc6222d56410035240e2d8be9fbbb0d70dabccad5c5efc5d4dacd602670a AUX pdb2pqr-1.4.0-gcc44.patch 229 RMD160 c5c1d51e6c695a3df8c04245a8d93168bef7a6b8 SHA1 5614b75a17b089624558026e51ba440479a5f658 SHA256 76a1bd592579d712bb6b22e6547edf1094d628e9d2b00b8d6ec89f8d9043c6df AUX pdb2pqr-1.4.0-install.patch 5372 RMD160 8d6c5f3c85ceea0562a767a3792228e6ff0eee96 SHA1 77a70693687be8d14eb3221ffc62a3daccc38f8e SHA256 e93025a88b5d6fff6e1fb45471471aef006d3074ece0b9cd9ff781736a2f1643 AUX pdb2pqr-1.4.0-ldflags.patch 1293 RMD160 47c2e4b484cf0936176683342afa6e89bb0b0712 SHA1 6c9088bbbf87a91c28fe6fdd39b3db097143f103 SHA256 cfab690b3c128b2c65e217893b546d6e56ffb2ffd7110872f352d6243f56f726 @@ -15,6 +15,6 @@ DIST pdb2pqr-1.4.0.tar.gz 5471743 RMD160 4d5596da5f9bdb2c657e7d0d88d91d20d00569e EBUILD pdb2pqr-1.1.2.ebuild 1887 RMD160 0f9fa1296696d9e6a1588830673ba8ae068ab1fd SHA1 ed35a726600197eec5e5b985a602d34c652ba301 SHA256 cd5fb2648e1c104fb3cec78df44ae7a554d7ac9a656995b99bd4267fa824145c EBUILD pdb2pqr-1.2.1.ebuild 1736 RMD160 3087df9d6f47e99d51f9dbb8014a442803d40182 SHA1 1b7b8f2cc68b0eca72469145769cecc69b79e7d2 SHA256 10cb0ef51344bc4eb29f5855e99c461befb532451f80fafaf0630532414b131a EBUILD pdb2pqr-1.3.0.ebuild 1981 RMD160 d9e8eb2f45aa12cd478e4e27e99ddf66aa202c5a SHA1 39de5c8e05de1827ab618959f73b256fd915fe8d SHA256 831d3e176306826bd44146f489030186beba521d00d7a87864ebb13272edfd17 -EBUILD pdb2pqr-1.4.0-r1.ebuild 2991 RMD160 2cbcf5561feba6cf51763e5998ac3dd719396dc0 SHA1 9d7016d1a22519d7557a74b42bd3f375e9e96ac5 SHA256 42543f03faebb1ed271ad6b0ced4f24f7ef752e416a70cb18722849b8ee23313 -MISC ChangeLog 2609 RMD160 fdc89855c085a3d6a054add537e1fedecfca848d SHA1 2944baae9647808c9e995a2a66dacc425275c7f5 SHA256 a4c849fda59361558c83bdf34e669760016d8ed828b461b92923eb10930c8a9c +EBUILD pdb2pqr-1.4.0-r1.ebuild 2771 RMD160 95b243244ebf8167bb3d1d3a233f52985046345a SHA1 5ee56fc36c834c8a11d5b06d5d57404c9c844435 SHA256 3dc0ffb3b9e414f15b6aaee11e03309ec40558ad001a0bd2225465a5da028a26 +MISC ChangeLog 2845 RMD160 fd9429385a718717868a3d716995d9fdf0a8245d SHA1 a8259e42ebca0c2dc8a4b02c787bd714323cf959 SHA256 020824489012e158f79112789673d5c3020dca01eb798d3b7586d81b3a783cbb MISC metadata.xml 239 RMD160 c9646b9b2171a8eeac8517b70efe2d2f8b6aa0f0 SHA1 48e78f37fbb221dc94978bf1ea4a9ba874a52464 SHA256 5dd1bfe10b60a7f631b103e6755e771471fea0334312522ef256db4ddb6923c2 diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch index f837e90390e3..addb76b9b4e6 100644 --- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch +++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch @@ -1,5 +1,6 @@ ---- configure.ac 2009-04-02 16:53:56.000000000 +0200 -+++ configure.ac.new 2009-04-22 11:41:28.000000000 +0200 +diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac +--- pdb2pqr-1.4.0/configure.ac 2009-04-02 10:53:56.000000000 -0400 ++++ pdb2pqr-1.4.0.new/configure.ac 2009-09-24 19:36:47.000000000 -0400 @@ -255,38 +255,6 @@ # Test for Numeric install @@ -39,7 +40,14 @@ # If failed, test for numpy AC_MSG_CHECKING([whether you defined numpy]) -@@ -463,23 +431,8 @@ +@@ -457,29 +425,14 @@ + HAVE_PDB2PQR_OPAL=1 + fi + +-if test "$PDB2PQR_OPAL_URL" != ""; then ++if test "$PDB2PQR_OPAL_URL" != "no"; then + HAVE_PDB2PQR_OPAL=1 + if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then echo ZSI is installed else # need to install ZSI @@ -65,8 +73,9 @@ fi fi ---- pdb2pka/NEWligand_topology.py 2007-10-12 21:52:40.000000000 +0200 -+++ pdb2pka/NEWligand_topology.py.new 2009-04-22 17:01:11.000000000 +0200 +diff -Naur pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py +--- pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py 2007-10-12 15:52:40.000000000 -0400 ++++ pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py 2009-09-24 19:36:07.000000000 -0400 @@ -3,10 +3,7 @@ # PC 2005/09/23 # Get ligand topologies @@ -79,8 +88,9 @@ from sets import Set from ligandclean.trial_templates import * ---- pdb2pka/ligand_topology.py 2008-06-13 16:15:38.000000000 +0200 -+++ pdb2pka/ligand_topology.py.new 2009-04-22 17:02:59.000000000 +0200 +diff -Naur pdb2pqr-1.4.0/pdb2pka/ligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py +--- pdb2pqr-1.4.0/pdb2pka/ligand_topology.py 2008-06-13 10:15:38.000000000 -0400 ++++ pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py 2009-09-24 19:36:07.000000000 -0400 @@ -3,10 +3,7 @@ # PC 2005/09/23 # Get ligand topologies diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild index 4dce16038bc2..0121e9bcee04 100644 --- a/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild +++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2009 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild,v 1.2 2009/05/24 16:17:18 mr_bones_ Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild,v 1.3 2009/09/24 23:43:11 markusle Exp $ inherit eutils fortran multilib flag-o-matic distutils python @@ -43,8 +43,6 @@ src_compile() { econf \ $(use_with opal) || \ die "econf failed" -#die -# $(use_with opal)="http://ws.nbcr.net/opal/services/pdb2pqr_1.4.0" || \ emake || die "emake failed" } @@ -55,9 +53,7 @@ src_test() { } src_install() { -# emake -j1 PREFIX="${D}"/$(python_get_sitedir)/${PN} install || die dodir $(python_get_sitedir)/${PN} -# emake -j1 DESTDIR="${D}"/$(python_get_sitedir)/${PN} install || die emake -j1 DESTDIR="${D}$(python_get_sitedir)/${PN}" PREFIX="" install || die if use doc; then |