sci-chemistry/gopenmol: Bump to EAPI=5 and new python eclass, fix for tcl8.6; fix implicit declarations; restrict license, #470782

Package-Manager: portage-2.2.0_alpha186/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

7 files changed, 243 insertions, 17 deletions

diff --git a/sci-chemistry/gopenmol/ChangeLog b/sci-chemistry/gopenmol/ChangeLog
index bbba41fd68f1..f1c8e356c0aa 100644
--- a/sci-chemistry/gopenmol/ChangeLog
+++ b/sci-chemistry/gopenmol/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/gopenmol
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gopenmol/ChangeLog,v 1.12 2012/04/02 06:06:41 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gopenmol/ChangeLog,v 1.13 2013/07/04 15:51:59 jlec Exp $
+
+*gopenmol-3.00-r3 (04 Jul 2013)
+
+  04 Jul 2013; Justin Lecher <jlec@gentoo.org> gopenmol-3.00-r2.ebuild,
+  +gopenmol-3.00-r3.ebuild, +files/3.00-impl-dec.patch,
+  +files/3.00-tcl8.6.patch, metadata.xml:
+  Bump to EAPI=5 and new python eclass, fix for tcl8.6; fix implicit
+  declarations; restrict license, #470782
 
   02 Apr 2012; Justin Lecher <jlec@gentoo.org> gopenmol-3.00-r2.ebuild,
   metadata.xml:
diff --git a/sci-chemistry/gopenmol/Manifest b/sci-chemistry/gopenmol/Manifest
index 6aa5e9675a82..bb78917d76b2 100644
--- a/sci-chemistry/gopenmol/Manifest
+++ b/sci-chemistry/gopenmol/Manifest
@@ -1,16 +1,29 @@
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 Hash: SHA512
 
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-AUX 3.00-multilib.patch 3745 RMD160 1113a0d44a0edb8e81f5ada89bec2ac0f7fc4a21 SHA1 620e158bf54b75d818c67277017562499f723068 SHA256 95388ce63c362c6573c49b3c7d5427ea4d18f6c949db3d4b0bbcf8fabe826125
-DIST gopenmol-3.00-linux.tar.gz 29615195 RMD160 8ed743925bf2c8583228fa19d8afbdc37c0af8de SHA1 8ab41ba3ae8cf2366bb1c2e03f9e23d5a5a72ce2 SHA256 314494a751f65c28d015fee854d2ee347fecbca6ccf31bb7e04db7eda6a16a23
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+DIST gopenmol-3.00-linux.tar.gz 29615195 SHA256 314494a751f65c28d015fee854d2ee347fecbca6ccf31bb7e04db7eda6a16a23 SHA512 e28fb607fcfdd543f4e62d3d1bf8ba789bafda608bb6a16e534bfd48bb4f2e2741a9fa98b7ead25db7d5572bb92064c73ba59987b0c3c3193477c3735babefd3 WHIRLPOOL eed5015c81b2c6e4cb14faf3f3176b979a3e79d1bb014dbd10fd606de0452f502b004b4bcb85e5cea57191ed782b3f9afeee5027c155d48370f8960cbca12d75
+EBUILD gopenmol-3.00-r2.ebuild 2231 SHA256 e3768a85e8a1601ab6b4e4a724fb4cefbdcb5d54abd7f0c2c2167b59a68f2090 SHA512 bd4975143382789395469e3a7a647ce9763414eb591058026b9133571480ebc16ced07f023c51c866abe31e4ab0bd716c641d886e73a14dbbbeef4c0ed8717d7 WHIRLPOOL a63049bbf5c1f4acc71b6397c05f0c5d836b359d7a256dab24056ab257c9daf09f473d78628551778a4b762bfddabcc86879bcd5926403cfbb68a25b80f932e2
+EBUILD gopenmol-3.00-r3.ebuild 2331 SHA256 08d06bdeaced61c7345e482c91c526dbf260b6cfc2add26625b03c939d957604 SHA512 143d2673876cd461dc10028ffbdab2bf6bd410d25480f06d93ba2437ebbf992729a37e75f20ddfa6436693c5a3c5314e3ae6176f5cad1d8d0b8109004c5699ce WHIRLPOOL e50d249055c14ae2785f1961ae4ac1193838a936548c264fe4f51dc007c41f36bb01767275a3ab5586e0706cd9538a33f4c4831908eca56383a0afd2fb680068
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diff --git a/sci-chemistry/gopenmol/files/3.00-impl-dec.patch b/sci-chemistry/gopenmol/files/3.00-impl-dec.patch
new file mode 100644
index 000000000000..e1d66c7aaa5d
--- /dev/null
+++ b/sci-chemistry/gopenmol/files/3.00-impl-dec.patch
@@ -0,0 +1,80 @@
+ density/density.c    | 1 +
+ utility/g94cub2pl.c  | 1 +
+ utility/gamess2plt.c | 1 +
+ utility/gcube2plt.c  | 1 +
+ utility/jaguar2plt.c | 1 +
+ vss/vssmod.c         | 1 +
+ 6 files changed, 6 insertions(+)
+
+diff --git a/density/density.c b/density/density.c
+index 130a48e..ee218c5 100755
+--- a/density/density.c
++++ b/density/density.c
+@@ -13,6 +13,7 @@
+ #include <string.h>
+ #include <sys/types.h>
+ #include <malloc.h>
++#include <stdlib.h>
+ 
+ #define VERBOSE    0
+ #define BUFF_LEN 500
+diff --git a/utility/g94cub2pl.c b/utility/g94cub2pl.c
+index e773ab2..94fbcfd 100755
+--- a/utility/g94cub2pl.c
++++ b/utility/g94cub2pl.c
+@@ -315,6 +315,7 @@ which can be read by gOpenMol or SCARECROW.
+ #include <sys/types.h>
+ #include <malloc.h>
+ #include <string.h>
++#include <stdlib.h>
+ 
+ #define BUFF_LEN        256
+ #define BOHR_RADIUS     0.52917715  /* conversion constant */
+diff --git a/utility/gamess2plt.c b/utility/gamess2plt.c
+index 3f6108e..5da481d 100755
+--- a/utility/gamess2plt.c
++++ b/utility/gamess2plt.c
+@@ -86,6 +86,7 @@ which can be read by gOpenMol or SCARECROW.
+ #include <sys/types.h>
+ #include <malloc.h>
+ #include <string.h>
++#include <stdlib.h>
+ 
+ #define BUFF_LEN        256
+ #define BOHR_RADIUS     0.52917715  /* conversion constant */
+diff --git a/utility/gcube2plt.c b/utility/gcube2plt.c
+index c5f7b5e..711bad3 100755
+--- a/utility/gcube2plt.c
++++ b/utility/gcube2plt.c
+@@ -306,6 +306,7 @@ which can be read by gOpenMol or SCARECROW.
+ #include <sys/types.h>
+ #include <malloc.h>
+ #include <string.h>
++#include <stdlib.h>
+ 
+ #define BUFF_LEN        256
+ #define BOHR_RADIUS     0.52917715  /* conversion constant */
+diff --git a/utility/jaguar2plt.c b/utility/jaguar2plt.c
+index 657128c..96d6ac1 100755
+--- a/utility/jaguar2plt.c
++++ b/utility/jaguar2plt.c
+@@ -26,6 +26,7 @@ fastes running coordinate.
+ #include <sys/types.h>
+ #include <malloc.h>
+ #include <string.h>
++#include <stdlib.h>
+ 
+ #define BUFF_LEN        256
+ #define BOHR_RADIUS     0.52917715  /* conversion constant */
+diff --git a/vss/vssmod.c b/vss/vssmod.c
+index 957d2e5..9d73978 100755
+--- a/vss/vssmod.c
++++ b/vss/vssmod.c
+@@ -20,6 +20,7 @@ C- for the potentials
+ #include <math.h>
+ #include <string.h>
+ #include <malloc.h>
++#include <stdlib.h>
+ 
+ #define LINE_LEN 80
+ #define BUFF_LEN 500
diff --git a/sci-chemistry/gopenmol/files/3.00-tcl8.6.patch b/sci-chemistry/gopenmol/files/3.00-tcl8.6.patch
new file mode 100644
index 000000000000..a4c3bce12468
--- /dev/null
+++ b/sci-chemistry/gopenmol/files/3.00-tcl8.6.patch
@@ -0,0 +1,32 @@
+ src/graphics/g_Mmain.c | 2 +-
+ src/parser/p_parser.c  | 4 ++--
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/src/graphics/g_Mmain.c b/src/graphics/g_Mmain.c
+index b9bb340..f044568 100755
+--- a/src/graphics/g_Mmain.c
++++ b/src/graphics/g_Mmain.c
+@@ -487,7 +487,7 @@ int gomp_Mmain(int argc, const char *argv[])
+     {
+         Tcl_Interp  *interp;
+         interp = gomp_GetTclInterp();
+-        sprintf(Temp,"'%s' problems creating the Tk window",interp->result);
++        sprintf(Temp,"'%s' problems creating the Tk window",Tcl_GetStringResult(interp));
+         gomp_PrintERROR(Temp);
+         return(1);
+     }
+diff --git a/src/parser/p_parser.c b/src/parser/p_parser.c
+index c9fd8ce..62eb05c 100755
+--- a/src/parser/p_parser.c
++++ b/src/parser/p_parser.c
+@@ -809,8 +809,8 @@ int          gomp_TclRunScript()
+     if(value != (const char *)NULL) {
+         code = Tcl_EvalFile(interp , value);
+         if(code != TCL_OK) {
+-            if(*interp->result != (char)NULL) {
+-                gomp_PrintERROR(interp->result);
++            if(*Tcl_GetStringResult(interp) != (char)NULL) {
++                gomp_PrintERROR(Tcl_GetStringResult(interp));
+                 return(1);
+             }
+         }
diff --git a/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild b/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild
index 7f5e4913bd89..d06498e19957 100644
--- a/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild
+++ b/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild
@@ -1,18 +1,18 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild,v 1.5 2012/04/02 06:06:41 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild,v 1.6 2013/07/04 15:51:59 jlec Exp $
 
 EAPI=4
 
 PYTHON_DEPEND="2"
 
-inherit eutils multilib prefix python
+inherit eutils multilib python
 
 DESCRIPTION="Tool for the visualization and analysis of molecular structures"
 HOMEPAGE="http://www.csc.fi/gopenmol/"
 SRC_URI="${HOMEPAGE}/distribute/${P}-linux.tar.gz"
 
-LICENSE="as-is"
+LICENSE="all-rights-reserved"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
@@ -31,6 +31,8 @@ RDEPEND="
 	x11-libs/libXxf86vm"
 DEPEND="${RDEPEND}"
 
+RESTRICT="mirror"
+
 S="${WORKDIR}/gOpenMol-${PV}/src"
 
 pkg_setup() {
diff --git a/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild b/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild
new file mode 100644
index 000000000000..fb0fdff6da5b
--- /dev/null
+++ b/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild
@@ -0,0 +1,91 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild,v 1.1 2013/07/04 15:51:59 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit eutils multilib python-single-r1
+
+DESCRIPTION="Tool for the visualization and analysis of molecular structures"
+HOMEPAGE="http://www.csc.fi/gopenmol/"
+SRC_URI="${HOMEPAGE}/distribute/${P}-linux.tar.gz"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	dev-lang/tk
+	dev-tcltk/bwidget
+	media-libs/freeglut
+	virtual/jpeg
+	virtual/opengl
+	x11-libs/libICE
+	x11-libs/libXau
+	x11-libs/libXdmcp
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXxf86vm"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+S="${WORKDIR}/gOpenMol-${PV}/src"
+
+src_prepare() {
+	cd ..
+	epatch \
+		"${FILESDIR}"/${PV}-include-config-for-plugins.patch \
+		"${FILESDIR}"/${PV}-multilib.patch \
+		"${FILESDIR}"/${PV}-tcl8.6.patch \
+		"${FILESDIR}"/${PV}-impl-dec.patch
+
+	sed \
+		-e "s:GENTOOLIBDIR:$(get_libdir):g" \
+		-i src/{config.mk.ac,plugins/config.mk.ac} || die
+	sed "/GOM_TEMP/s:^.*$:GOM_TEMP=\"${EPREFIX}/tmp/:g" -i environment.txt || die
+}
+
+src_compile() {
+	default
+
+	# Plugins and Utilities are not built by default
+	cd "${S}"/plugins && emake
+	cd "${S}"/utility && emake
+}
+
+src_install() {
+	einstall
+
+	cd "${S}"/plugins && einstall
+	cd "${S}"/utility && einstall
+
+	dosym ../$(get_libdir)/gOpenMol-${PV}/bin/${PN} /usr/bin/${PN}
+
+	dodoc "${ED}"/usr/share/gOpenMol-${PV}/{docs/*,README*} || die
+
+	dodir /usr/share/doc/${PF}/html
+	mv -T "${ED}"/usr/share/gOpenMol-${PV}/help "${ED}"/usr/share/doc/${PF}/html || die
+	mv "${ED}"/usr/share/gOpenMol-${PV}/utility "${ED}"/usr/share/doc/${PF}/html || die
+
+	rm -rf \
+		"${ED}"/usr/$(get_libdir)/gOpenMol-${PV}/{src,install} \
+		"${ED}"/usr/share/gOpenMol-${PV}/{docs,README*,COPYRIGHT} || die
+
+	cat >> "${T}"/20${PN} <<- EOF
+	GOM_ROOT="${EPREFIX}"/usr/$(get_libdir)/gOpenMol-${PV}/
+	GOM_DATA="${EPREFIX}"/usr/share/gOpenMol-${PV}/data
+	GOM_HELP="${EPREFIX}"/usr/share/doc/${PVR}/html
+	GOM_DEMO="${EPREFIX}"/usr/share/gOpenMol-${PV}/demo
+	EOF
+
+	doenvd "${T}"/20${PN}
+}
+
+pkg_postinst() {
+	einfo "Run gOpenMol using the rungOpenMol script."
+}
diff --git a/sci-chemistry/gopenmol/metadata.xml b/sci-chemistry/gopenmol/metadata.xml
index e42d0af60f42..51fdedab1b38 100644
--- a/sci-chemistry/gopenmol/metadata.xml
+++ b/sci-chemistry/gopenmol/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
+  <herd>sci-chemistry</herd>
 </pkgmetadata>