proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

8 files changed, 416 insertions, 0 deletions

diff --git a/sci-chemistry/gopenmol/Manifest b/sci-chemistry/gopenmol/Manifest
new file mode 100644
index 000000000000..087c602229b0
--- /dev/null
+++ b/sci-chemistry/gopenmol/Manifest
@@ -0,0 +1 @@
+DIST gopenmol-3.00-linux.tar.gz 29615195 SHA256 314494a751f65c28d015fee854d2ee347fecbca6ccf31bb7e04db7eda6a16a23 SHA512 e28fb607fcfdd543f4e62d3d1bf8ba789bafda608bb6a16e534bfd48bb4f2e2741a9fa98b7ead25db7d5572bb92064c73ba59987b0c3c3193477c3735babefd3 WHIRLPOOL eed5015c81b2c6e4cb14faf3f3176b979a3e79d1bb014dbd10fd606de0452f502b004b4bcb85e5cea57191ed782b3f9afeee5027c155d48370f8960cbca12d75
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-include-config-for-plugins.patch b/sci-chemistry/gopenmol/files/3.00-include-config-for-plugins.patch
new file mode 100644
index 000000000000..a8602d07a03e
--- /dev/null
+++ b/sci-chemistry/gopenmol/files/3.00-include-config-for-plugins.patch
@@ -0,0 +1,11 @@
+--- gOpenMol-3.00.orig/src/plugins/Makefile	2005-12-02 19:38:08.000000000 -0800
++++ gOpenMol-3.00/src/plugins/Makefile	2005-12-02 19:37:29.000000000 -0800
+@@ -8,6 +8,8 @@
+ #          Coded by: Eero Häkkinen
+ ##############################################################################
+ 
++include config.mk
++
+ build-all: build FORCE ;
+ 
+ all install install-local uninstall: FORCE
diff --git a/sci-chemistry/gopenmol/files/3.00-multilib.patch b/sci-chemistry/gopenmol/files/3.00-multilib.patch
new file mode 100644
index 000000000000..9ca263808622
--- /dev/null
+++ b/sci-chemistry/gopenmol/files/3.00-multilib.patch
@@ -0,0 +1,104 @@
+diff --git a/src/config.mk.ac b/src/config.mk.ac
+index b1061d9..374bc77 100755
+--- a/src/config.mk.ac
++++ b/src/config.mk.ac
+@@ -18,7 +18,7 @@ gomroot          = $(libdir)/$(gomsubdir)
+ gomdataroot      = $(datadir)/$(gomsubdir)
+ gombindir        = $(gomroot)/bin
+ gomincdir        = $(includedir)/$(gomsubdir)
+-gomlibdir        = $(gomroot)/bin
++gomlibdir        = $(gomroot)/GENTOOLIBDIR
+ # Tcl/Tk entries.
+ TCL_LIBRARY      = @TCL_LIBRARY@
+ TK_LIBRARY       = @TK_LIBRARY@
+diff --git a/src/plugins/Makefile b/src/plugins/Makefile
+index bb9af64..cf8a97d 100755
+--- a/src/plugins/Makefile
++++ b/src/plugins/Makefile
+@@ -22,7 +22,7 @@ all install install-local uninstall: FORCE
+ build compile clean clean-libs clean-objs: FORCE
+ 	-@for dir in *; do \
+ 	    if test -f "$$dir/Makefile"; then \
+-		( cd "$$dir" && $(MAKE) $(MFLAGS) $@ ) ;\
++		( cd "$$dir" && $(MAKE) $(MFLAGS) $@ ) || exit 1;\
+ 	    fi ;\
+ 	done
+ 
+diff --git a/src/plugins/config.mk.ac b/src/plugins/config.mk.ac
+index 03e3f6b..eb30ea8 100755
+--- a/src/plugins/config.mk.ac
++++ b/src/plugins/config.mk.ac
+@@ -11,7 +11,7 @@ gomdataroot      = ${datadir}/${gomsubdir}
+ gombindir        = ${gomroot}/bin
+ gomincdir        = ${gomsrcdir}/include/gomlib
+ #INS gomincdir        = ${includedir}/${gomsubdir}
+-gomlibdir        = ${gomroot}/bin
++gomlibdir        = ${gomroot}/GENTOOLIBDIR
+ gomsrcdir        = @abs_top_srcdir@
+ gombltdir        = @abs_top_builddir@
+ #INS gomsrcdir        = ${gomroot}/src
+diff --git a/src/plugins/rules.mk b/src/plugins/rules.mk
+index d41ed47..da133c6 100755
+--- a/src/plugins/rules.mk
++++ b/src/plugins/rules.mk
+@@ -43,12 +43,12 @@ $(LIBRARY): $(libdeps)
+ 	@$(RM) alldeps.dT
+ 
+ link-CC: FORCE
+-	$(GOM_LINK_CC) $(PLUG_CFLAGS) -o $(LIBRARY) $(OBJECTS) \
+-	    $(PLUG_LDFLAGS) $(PLUG_LIBS) $(GOM_LINKFLAGS)
++	$(GOM_LINK_CC) $(GOM_LINKFLAGS) $(PLUG_CFLAGS) -o $(LIBRARY) $(OBJECTS) \
++	    $(PLUG_LDFLAGS) $(PLUG_LIBS)
+ 
+ link-CXX: FORCE
+-	$(GOM_LINK_CXX) $(PLUG_CXXFLAGS) -o $(LIBRARY) $(OBJECTS) \
+-	    $(PLUG_LDFLAGS) $(PLUG_LIBS) $(GOM_LINKFLAGS)
++	$(GOM_LINK_CXX) $(GOM_LINKFLAGS) $(PLUG_CXXFLAGS) -o $(LIBRARY) $(OBJECTS) \
++	    $(PLUG_LDFLAGS) $(PLUG_LIBS)
+ 
+ # Rule to compile the source files.
+ # First make:
+diff --git a/src/unix/make/install.mk b/src/unix/make/install.mk
+index 3018946..98c061a 100755
+--- a/src/unix/make/install.mk
++++ b/src/unix/make/install.mk
+@@ -36,7 +36,7 @@ mkinstalldirs: mkinstalldirs-local mkinstalldirs-shared FORCE ;
+ mkinstalldirs-local: FORCE
+ 	$(MKDIR_P) '$(gomroot)' || test -d '$(gomroot)'
+ 	@$(set_show); set -e; \
+-	for dir in bin src/plugins src/unix; do \
++	for dir in bin lib src/plugins src/unix; do \
+ 	    dir='$(gomroot)'/$$dir; \
+ 	    $$show $(MKDIR_P) "$$dir"; \
+ 	    $(MKDIR_P) "$$dir" || test -d "$$dir"; \
+diff --git a/src/unix/make/utility.mk.ac b/src/unix/make/utility.mk.ac
+index 21ad59d..ee25ac7 100755
+--- a/src/unix/make/utility.mk.ac
++++ b/src/unix/make/utility.mk.ac
+@@ -47,8 +47,7 @@ BINARIES_F   = ambera2b$(EXEEXT) \
+                xmol2bamber$(EXEEXT) \
+                xplor2charmm$(EXEEXT) \
+                gridasc2plt$(EXEEXT) \
+-               gridbin2plt$(EXEEXT) \
+-               icon8$(EXEEXT)
++               gridbin2plt$(EXEEXT)
+ 
+ BINARIES_JAR = xvibs.jar
+ 
+@@ -76,13 +75,13 @@ $(OBJECTS_C):
+ 	$(CC) -c $? $(CPPFLAGS) $(CFLAGS)
+ 
+ $(BINARIES_C):
+-	$(CC) -o $@ $? $(CPPFLAGS) $(CFLAGS) $(STD_LIBS) $(LDFLAGS)
++	$(CC) $(LDFLAGS) -o $@ $? $(CPPFLAGS) $(CFLAGS) $(STD_LIBS)
+ 
+ $(BINARIES_CXX):
+-	$(CXX) -o $@ $? $(CPPFLAGS) $(CXXFLAGS) $(STD_LIBS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o $@ $? $(CPPFLAGS) $(CXXFLAGS) $(STD_LIBS)
+ 
+ $(BINARIES_F):
+-	$(F77) -o $@ $? $(FFLAGS) $(STD_LIBS) $(LDFLAGS)
++	$(F77) $(LDFLAGS) -o $@ $? $(FFLAGS) $(STD_LIBS)
+ 
+ $(BINARIES_JAR):
+ 	cp $? $@
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
new file mode 100644
index 000000000000..1a50d785d368
--- /dev/null
+++ b/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+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="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	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-${PV}/src"
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-include-config-for-plugins.patch \
+		"${FILESDIR}"/${PV}-multilib.patch
+
+	sed \
+		-e "s:GENTOOLIBDIR:$(get_libdir):g" \
+		-i 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/gopenmol-3.00-r3.ebuild b/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild
new file mode 100644
index 000000000000..b936d437e5a0
--- /dev/null
+++ b/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild
@@ -0,0 +1,91 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_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
new file mode 100644
index 000000000000..51fdedab1b38
--- /dev/null
+++ b/sci-chemistry/gopenmol/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+</pkgmetadata>