Fixed automagic patch to honor --without-opal (fixes bug #278199).

Package-Manager: portage-2.1.6.13/cvs/Linux x86_64

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