Remove masked for removal packages

8 files changed, 0 insertions, 419 deletions

diff --git a/sci-chemistry/gopenmol/Manifest b/sci-chemistry/gopenmol/Manifest
deleted file mode 100644
index 087c602229b0..000000000000
--- a/sci-chemistry/gopenmol/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index e1d66c7aaa5d..000000000000
--- a/sci-chemistry/gopenmol/files/3.00-impl-dec.patch
+++ /dev/null
@@ -1,80 +0,0 @@
- 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
deleted file mode 100644
index a8602d07a03e..000000000000
--- a/sci-chemistry/gopenmol/files/3.00-include-config-for-plugins.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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
deleted file mode 100644
index 9ca263808622..000000000000
--- a/sci-chemistry/gopenmol/files/3.00-multilib.patch
+++ /dev/null
@@ -1,104 +0,0 @@
-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
deleted file mode 100644
index a4c3bce12468..000000000000
--- a/sci-chemistry/gopenmol/files/3.00-tcl8.6.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- 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
deleted file mode 100644
index 1a50d785d368..000000000000
--- a/sci-chemistry/gopenmol/gopenmol-3.00-r2.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# 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
deleted file mode 100644
index b936d437e5a0..000000000000
--- a/sci-chemistry/gopenmol/gopenmol-3.00-r3.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# 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
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/gopenmol/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>