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Fix for missing StripXml, #375903
authorJustin Lecher <jlec@gentoo.org>
Sat, 23 Jul 2011 12:29:01 +0000 (12:29 +0000)
committerJustin Lecher <jlec@gentoo.org>
Sat, 23 Jul 2011 12:29:01 +0000 (12:29 +0000)
Package-Manager: portage-2.2.0_alpha46/cvs/Linux x86_64

sci-chemistry/balbes/ChangeLog patch | blob | history
sci-chemistry/balbes/Manifest patch | blob | history
sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild [moved from sci-chemistry/balbes/balbes-1.0.0_p100317-r1.ebuild with 58% similarity] patch | blob | history
sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch [new file with mode: 0644] patch | blob
sci-chemistry/balbes/metadata.xml patch | blob | history

diff --git a/sci-chemistry/balbes/ChangeLog b/sci-chemistry/balbes/ChangeLog
index 3c56c20d2353f46ea954ec27d870e8ed2a5014a8..eb69efa205ab164ad8d5c96ce902e8fb8b4cb98f 100644 (file)
--- a/sci-chemistry/balbes/ChangeLog
+++ b/sci-chemistry/balbes/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/balbes
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/balbes/ChangeLog,v 1.8 2011/06/21 16:05:18 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/balbes/ChangeLog,v 1.9 2011/07/23 12:29:01 jlec Exp $
+
+*balbes-1.0.0_p100317-r2 (23 Jul 2011)
+
+  23 Jul 2011; Justin Lecher <jlec@gentoo.org>
+  +files/pyxml-0.8.4-python-2.6.patch, -balbes-1.0.0_p100317-r1.ebuild,
+  +balbes-1.0.0_p100317-r2.ebuild, metadata.xml:
+  Fix for missing StripXml, #375903
 
   21 Jun 2011; Justin Lecher <jlec@gentoo.org> balbes-1.0.0_p100317-r1.ebuild:
   Add dependency on virtual/fortran
diff --git a/sci-chemistry/balbes/Manifest b/sci-chemistry/balbes/Manifest
index b962054740324c641734f0e5c35e23bac0c46445..637efbcbf3ca2c13632901f288b678506274132e 100644 (file)
--- a/sci-chemistry/balbes/Manifest
+++ b/sci-chemistry/balbes/Manifest
@@ -1,16 +1,17 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
 AUX 1.0.0_p100317-makefile.patch 5150 RMD160 c2f167b02a475543cec7fd67d95a0fff563dede3 SHA1 4139dcaf29c46eff7be3a3b3e9af253e97be8ce3 SHA256 e25ec095918f38c99972896a48db6a0b0b1df36ba0a7a337acae7aa9c46bbbda
+AUX pyxml-0.8.4-python-2.6.patch 1749 RMD160 f8eb2f581a953e8a2b2968cea9a88fe5a1353243 SHA1 787a92081dd172aa36d5c52344e74ef922073bc0 SHA256 03c4eb073c58e7c28a22ff702a296ba4c4fe11a64d931ada6216d1876c6118e8
 DIST balbes-1.0.0_p100317.tar.gz 506464 RMD160 5fbb018b33d539734b5421951178c62847f58acf SHA1 a6907d1762c12c63f71bfb9fbb9d601d4271cda6 SHA256 c5bf6c2086e1a3d7d380e5501c0cffdb91cbf77c74d2951dd345273f21921d0c
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 RMD160 e9b7deb0766fb95d5e8946881f20e086f0896fe9 SHA1 ee5ada892694db5dc9b2d7d2330b4ac694f56580 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324
-EBUILD balbes-1.0.0_p100317-r1.ebuild 1452 RMD160 a5313f46a1082ffe6f724a046859d25ba7cbecef SHA1 61c08f7a1770e8469768384ac8e2512e1ceb59ea SHA256 4be46cd142aaef94fdb0651c70f5f1115f7e06786e6630d283038045cc53f27c
-MISC ChangeLog 1343 RMD160 33792b87442b671c676a8547a9e1a7bf12664381 SHA1 150f14de9668327dbe63f3a1b972e3ba6a1c767f SHA256 adbaf0591430b8df1c4583179ca14c36ac21933143253639af211b788a044e19
-MISC metadata.xml 770 RMD160 f1e7baae6a60a873a63aec933ffed69ea2187869 SHA1 34ce68dd6391227c5a2473732aaff8908430c29b SHA256 c09e937b404277aa8d72dbc3a51022b872a01c11ebf5271254aa6349c06eef44
+EBUILD balbes-1.0.0_p100317-r2.ebuild 2193 RMD160 bf3040693da4d6a925096cfc6e01f54d69aba681 SHA1 a6bb9746c4c6304ce97e492d557380773808acf7 SHA256 781e64dfe7fe93020a667132fab6ae3ad294e0809dbd47c68f3f57f66a56a7d5
+MISC ChangeLog 1588 RMD160 7e367d092a90c29364dabf5f900c87c86cee4362 SHA1 a9fb0433eeeea6b4d04ccb40aff1a9e2807e7488 SHA256 0d3aa07cb774dd06bf5e7ead033604acbf1a264006553a04a4aaf7ded8e7af73
+MISC metadata.xml 773 RMD160 55094bffdb9217dc73a9a7bfda9a57af5c797b58 SHA1 7b695d7c177eeb519e3ad58f1f4222e5f13fa29a SHA256 8decc10d9755c6134cd8f64bf4fbae5b5dd3c7bb04c5234dcbbf620a5e7bacc3
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAk4AwT8ACgkQgAnW8HDreRaS/gCgqwUVBIsKwHID/93AguyzeNSS
-OLYAoNBzrLQhae8GgHUJLrjg/hS6bvDf
-=qfiF
+iEYEAREKAAYFAk4qvpgACgkQgAnW8HDreRZA6gCgmTM+F0iqttHuo0SrvM97Xui2
+SvQAn2xD8HatbvEnfCWZ47AYwvSLqA5s
+=lIbN
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/balbes/balbes-1.0.0_p100317-r1.ebuild b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild
similarity index 58%
rename from sci-chemistry/balbes/balbes-1.0.0_p100317-r1.ebuild
rename to sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild
index e30fc1e2c0f3f2f268fc3c53457a52ac300a1743..bd15687e2870185efacf296b60e3f3b8db50b637 100644 (file)
--- a/sci-chemistry/balbes/balbes-1.0.0_p100317-r1.ebuild
+++ b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/balbes/balbes-1.0.0_p100317-r1.ebuild,v 1.5 2011/06/21 16:05:18 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild,v 1.1 2011/07/23 12:29:01 jlec Exp $
 
-EAPI="3"
+EAPI=3
 
 CCP4VER="6.1.3"
 PYTHON_DEPEND="2"
@@ -20,6 +20,8 @@ KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
 LICENSE="ccp4"
 IUSE=""
 
+# bundled PyXML is modified and cannot be replaced
+
 COMMON_DEPEND="
        sci-libs/ccp4-libs
        virtual/fortran"
@@ -39,23 +41,43 @@ pkg_setup() {
 
 src_unpack() {
        unpack ${P}.tar.gz
-       tar xvzf "${DISTDIR}"/ccp4-${CCP4VER}-core-src.tar.gz ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes
+       tar xvzf "${DISTDIR}"/ccp4-${CCP4VER}-core-src.tar.gz \
+               ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \
+               ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4
        python_convert_shebangs 2 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes
 }
 
 src_prepare() {
        mkdir "${WORKDIR}"/bin || die
        epatch "${FILESDIR}"/${PV}-makefile.patch
+       cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/
+       epatch "${FILESDIR}"/pyxml-0.8.4-python-2.6.patch
 }
 
 src_compile() {
        emake \
                BLANC_FORT="$(tc-getFC) ${FFLAGS}" || die
+       cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4
+       find build -delete
+       $(PYTHON) setup.py build
+       find xml/xslt test -delete
 }
 
 src_install() {
+       insinto /usr/share/balbes/BALBES_0.0.1/
+       doins -r \
+                "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \
+                "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 || die
        dobin \
                "${WORKDIR}"/bin/* \
                "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes \
                || die
 }
+
+pkg_postinst() {
+       python_mod_optimize /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4}
+}
+
+pkg_postrm() {
+       python_mod_cleanup /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4}
+}
diff --git a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch
new file mode 100644 (file)
index 0000000..d29b0b6
--- /dev/null
+++ b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch
@@ -0,0 +1,28 @@
+diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py
+--- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:54:36.000000000 +0900
++++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py     2008-12-15 16:57:02.000000000 +0900
+@@ -24,8 +24,8 @@ class ParsedAbbreviatedAbsoluteLocationP
+         self._rel = rel
+         nt = ParsedNodeTest.ParsedNodeTest('node', '')
+         ppl = ParsedPredicateList.ParsedPredicateList([])
+-        as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
+-        self._step = ParsedStep.ParsedStep(as, nt, ppl)
++        as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
++        self._step = ParsedStep.ParsedStep(as_, nt, ppl)
+         return
+ 
+     def evaluate(self, context):
+diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py
+--- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:54:36.000000000 +0900
++++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py     2008-12-15 16:58:58.000000000 +0900
+@@ -28,8 +28,8 @@ class ParsedAbbreviatedRelativeLocationP
+         self._right = right
+         nt = ParsedNodeTest.ParsedNodeTest('node','')
+         ppl = ParsedPredicateList.ParsedPredicateList([])
+-        as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
+-        self._middle = ParsedStep.ParsedStep(as, nt, ppl)
++        as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
++        self._middle = ParsedStep.ParsedStep(as_, nt, ppl)
+ 
+     def evaluate(self, context):
+         res = []
diff --git a/sci-chemistry/balbes/metadata.xml b/sci-chemistry/balbes/metadata.xml
index deb657090e7d3ecb925a7c5c6fdf77249a9ecc96..4bb6be5e5d0c0babab08b5d588fa418c99a26d18 100644 (file)
--- a/sci-chemistry/balbes/metadata.xml
+++ b/sci-chemistry/balbes/metadata.xml
@@ -2,10 +2,10 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
        <herd>sci-chemistry</herd>
-<maintainer>
-  <email>jlec@gentoo.org</email>
-</maintainer>
-<longdescription>
+       <maintainer>
+               <email>jlec@gentoo.org</email>
+       </maintainer>
+       <longdescription>
        BALBES is a system for solving protein structures using x-ray 
        crystalographic data. Molecular Replacement(MR) is its core 
        scientific method. BALBES aims to integrate all components, 
Unnamed repository; edit this file 'description' to name the repository.