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

10 files changed, 281 insertions, 0 deletions

diff --git a/sci-chemistry/molden/Manifest b/sci-chemistry/molden/Manifest
new file mode 100644
index 000000000000..e78207790325
--- /dev/null
+++ b/sci-chemistry/molden/Manifest
@@ -0,0 +1,2 @@
+DIST molden4.8.tar.gz 2969701 SHA256 314d9b9bdede2fd63d1e2f26e0212711576952244634fc28ea6c97ce2f7029b1 SHA512 11f2406e54a077d044369b5eee4a8a1c1b10f052188d33d4162af0151a1e76a1d5274d8788bbc3610905ff271b0bd2100990b77540a0290ad608bd5c29b839e3 WHIRLPOOL 838d66a4e17651dfd2bab893fa9b36ca8d722c879b9f10adb00c3c4e59974ae73e13060e6a559286c651ab35e1cea084049677277cc4b455e68a95c6c210dcf9
+DIST molden5.0.tar.gz 3063244 SHA256 c9cf8f656adf2f2c7a8b8b64fa07b5feaa9c3ca36c4803e1f58ac33de1cffdc4 SHA512 bf45849bf4efb67bc552767c28a6df6e5106a7d8ac2d73db2c7218412fb6cd2f2785c2be83a8589a5664ba9c0ca052cef5eb155c665ee1f3d6c7fe208f806a6b WHIRLPOOL ab7f1118b000a8df36cbaf23fddabb21bd291a2388e3aa5599e609ffa792bec01bf7df52a98f7e70125b504f7866e48ec6d5ce029ecd0e40c7bab7b8627c5c86
diff --git a/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch
new file mode 100644
index 000000000000..dd5aba4f17da
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch
@@ -0,0 +1,12 @@
+diff --git a/silly.c b/silly.c
+index 57d07e8..102156a 100644
+--- a/silly.c
++++ b/silly.c
+@@ -13,6 +13,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <math.h>
++#include <string.h>
+ 
+ #ifndef WIN32
+ #include <GL/gl.h>
diff --git a/sci-chemistry/molden/files/molden-4.8-ambfor.patch b/sci-chemistry/molden/files/molden-4.8-ambfor.patch
new file mode 100644
index 000000000000..1ececa7f57e9
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.8-ambfor.patch
@@ -0,0 +1,12 @@
+diff -Naur molden4.8/ambfor/makefile molden4.8.new/ambfor/makefile
+--- molden4.8/ambfor/makefile	2009-12-19 06:14:32.000000000 -0500
++++ molden4.8.new/ambfor/makefile	2010-02-25 22:33:41.000000000 -0500
+@@ -32,7 +32,7 @@
+ 	$(LDR) -o ambmd md.o verlet.o allocmd.o $(OBJS) $(LIBS)
+ 
+ ambfor.o:	ambfor.f
+-	${FC} -c -g -ffast-math -funroll-loops -m32 -o ambfor.o ambfor.f
++	${FC} $(FFLAGS) -c ambfor.f -o ambfor.o 
+ 
+ allocmd.o:	alloc.c
+ 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o
diff --git a/sci-chemistry/molden/files/molden-4.8-ldflags.patch b/sci-chemistry/molden/files/molden-4.8-ldflags.patch
new file mode 100644
index 000000000000..92fa6c665f3f
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.8-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/makefile b/makefile
+index 81147a3..9e2353e 100644
+--- a/makefile
++++ b/makefile
+@@ -224,10 +224,10 @@ all:	molden gmolden ambfor/ambfor ambfor/ambmd surf/surf
+ 
+ 
+ molden:	$(OBJS) mpdum.o xwin.o 
+-	$(LDR) -o molden $(OBJS) mpdum.o xwin.o $(LIBS)
++	$(LDR) $(LDFLAGS) -o molden $(OBJS) mpdum.o xwin.o $(LIBS)
+ 
+ gmolden:	$(OBJS) mpdum.o xwingl.o 
+-	$(LDR) -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG)
++	$(LDR) $(LDFLAGS)  -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG)
+ 
+ ambfor/ambfor:	ambfor/*.f ambfor/*.c
+ 	$(MAKE) -C ambfor FC=${FC} FFLAGS="${FFLAGS}" LDR="${LDR}" CFLAGS="${CFLAGS}"
+@@ -269,7 +269,7 @@ short_wrl:	short_wrl.o
+ # Moldens OpenGL helper program
+ 
+ moldenogl:	oglmol.o silly.o
+-	$(CC) -o moldenogl oglmol.o silly.o $(LIBSOGL)
++	$(CC) $(LDFLAGS) -o moldenogl oglmol.o silly.o $(LIBSOGL)
+ 
+ # conversion of CADPAC output to molden format
+ 
diff --git a/sci-chemistry/molden/files/molden-4.8-overflow.patch b/sci-chemistry/molden/files/molden-4.8-overflow.patch
new file mode 100644
index 000000000000..7cbd7f436f57
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.8-overflow.patch
@@ -0,0 +1,38 @@
+ xwin.c |   10 ++++++----
+ 1 files changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/xwin.c b/xwin.c
+index f395909..092edff 100644
+--- a/xwin.c
++++ b/xwin.c
+@@ -13552,7 +13552,7 @@ void NewActiveStruct()
+ #ifdef CRAY
+     _fcd ztr;
+ #else
+-    char ztr;
++    char ztr[4];
+ #endif
+ #endif
+ 
+@@ -13650,8 +13650,10 @@ void NewActiveStruct()
+ */
+ 	clfpstr->ihashz = 0;
+ #else
+-	strncpy(&ztr,HetAtm[j],3);
+-	parhet_(&j1,&ztr);
++	if (HetAtm[j] != NULL) {
++	   strncpy(ztr,HetAtm[j],3);
++	   parhet_(&j1,ztr);
++	}
+ #endif
+ #endif
+     }
+@@ -27353,7 +27355,7 @@ char *errstr;
+ 	UpdateZME();
+ 	RedrawScroll(&zscroll);
+     }
+-    strcpy(ZMEerr,errstr);
++    strncpy(ZMEerr,errstr,MAXZMEERR);
+     RedrawStatus();
+ }
+ 
diff --git a/sci-chemistry/molden/files/molden-5.0-ambfor.patch b/sci-chemistry/molden/files/molden-5.0-ambfor.patch
new file mode 100644
index 000000000000..9656ff7a79be
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-5.0-ambfor.patch
@@ -0,0 +1,16 @@
+ ambfor/makefile |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/ambfor/makefile b/ambfor/makefile
+index 8627a11..dbc23a1 100644
+--- a/ambfor/makefile
++++ b/ambfor/makefile
+@@ -47,7 +47,7 @@ ambmd:	md.o verlet.o qvdw.o allocmd.o $(OBJS)
+ 	$(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS)
+ 
+ ambfor.o:	ambfor.f
+-	${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f
++	${FC} $(FFLAGS) -c -o ambfor.o ambfor.f
+ 
+ allocmd.o:	alloc.c
+ 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o
diff --git a/sci-chemistry/molden/files/molden-5.0-overflow.patch b/sci-chemistry/molden/files/molden-5.0-overflow.patch
new file mode 100644
index 000000000000..4fc406266935
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-5.0-overflow.patch
@@ -0,0 +1,16 @@
+ xwin.c |   10 ++++++----
+ 1 files changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/xwin.c b/xwin.c
+index f395909..092edff 100644
+--- a/xwin.c
++++ b/xwin.c
+@@ -27353,7 +27355,7 @@ char *errstr;
+ 	UpdateZME();
+ 	RedrawScroll(&zscroll);
+     }
+-    strcpy(ZMEerr,errstr);
++    strncpy(ZMEerr,errstr,MAXZMEERR);
+     RedrawStatus();
+ }
+ 
diff --git a/sci-chemistry/molden/metadata.xml b/sci-chemistry/molden/metadata.xml
new file mode 100644
index 000000000000..51fdedab1b38
--- /dev/null
+++ b/sci-chemistry/molden/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>
diff --git a/sci-chemistry/molden/molden-4.8-r2.ebuild b/sci-chemistry/molden/molden-4.8-r2.ebuild
new file mode 100644
index 000000000000..943f7cc4fb05
--- /dev/null
+++ b/sci-chemistry/molden/molden-4.8-r2.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils fortran-2 flag-o-matic toolchain-funcs
+
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac"
+HOMEPAGE="http://www.cmbi.kun.nl/~schaft/molden/molden.html"
+SRC_URI="ftp://ftp.cmbi.kun.nl/pub/molgraph/${PN}/${MY_P}.tar.gz"
+
+LICENSE="MOLDEN"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="opengl"
+
+RDEPEND="
+	x11-libs/libXmu
+		virtual/glu
+	opengl? (
+		media-libs/freeglut
+		virtual/opengl )"
+DEPEND="${RDEPEND}
+	x11-misc/gccmakedep
+	app-editors/vim"
+	# vim provides ex, which the build system uses (surf/Makefile, at least)
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-ambfor.patch \
+		"${FILESDIR}"/${P}-overflow.patch \
+		"${FILESDIR}"/${P}-ldflags.patch \
+		"${FILESDIR}"/${PN}-4.7-implicit-dec.patch
+	sed \
+		-e 's:makedepend:gccmakedep:g' \
+		-e "s:/usr/include/sgidefs.h::g" \
+		-i surf/Makefile || die
+	sed 's:shell g77:shell $(FC):g' -i makefile || die
+}
+
+src_compile() {
+	# Use -mieee on alpha, according to the Makefile
+	use alpha && append-flags -mieee
+
+	# Honor CC, CFLAGS, FC, and FFLAGS from environment;
+	# unfortunately a bash bug prevents us from doing typeset and
+	# assignment on the same line.
+	typeset -a args
+	args=(
+			CC="$(tc-getCC) ${CFLAGS}" \
+			FC="$(tc-getFC)" \
+			LDR="$(tc-getFC)" \
+			FFLAGS="${FFLAGS}" )
+
+	einfo "Building Molden..."
+	emake -j1 "${args[@]}"
+	if use opengl ; then
+		einfo "Building Molden OpenGL helper..."
+		emake -j1 "${args[@]}" moldenogl
+	fi
+}
+
+src_install() {
+	dobin ${PN} g${PN}
+	if use opengl ; then
+		dobin ${PN}ogl
+	fi
+
+	dodoc HISTORY README REGISTER
+	cd doc
+	uncompress * && dodoc *
+}
diff --git a/sci-chemistry/molden/molden-5.0.ebuild b/sci-chemistry/molden/molden-5.0.ebuild
new file mode 100644
index 000000000000..e4ad3b6d802d
--- /dev/null
+++ b/sci-chemistry/molden/molden-5.0.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils fortran-2 flag-o-matic toolchain-funcs
+
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac"
+HOMEPAGE="http://www.cmbi.kun.nl/~schaft/molden/molden.html"
+SRC_URI="ftp://ftp.cmbi.kun.nl/pub/molgraph/${PN}/${MY_P}.tar.gz"
+
+LICENSE="MOLDEN"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="opengl"
+
+RDEPEND="
+	x11-libs/libXmu
+		virtual/glu
+	opengl? (
+		media-libs/freeglut
+		virtual/opengl )"
+DEPEND="${RDEPEND}
+	x11-misc/gccmakedep
+	app-editors/vim"
+	# vim provides ex, which the build system uses (surf/Makefile, at least)
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-ambfor.patch \
+		"${FILESDIR}"/${P}-overflow.patch \
+		"${FILESDIR}"/${PN}-4.8-ldflags.patch \
+		"${FILESDIR}"/${PN}-4.7-implicit-dec.patch
+	sed \
+		-e 's:makedepend:gccmakedep:g' \
+		-e "s:/usr/include/sgidefs.h::g" \
+		-i surf/Makefile || die
+	sed 's:shell g77:shell $(FC):g' -i makefile || die
+}
+
+src_compile() {
+	# Use -mieee on alpha, according to the Makefile
+	use alpha && append-flags -mieee
+
+	# Honor CC, CFLAGS, FC, and FFLAGS from environment;
+	# unfortunately a bash bug prevents us from doing typeset and
+	# assignment on the same line.
+	typeset -a args
+	args=(
+			CC="$(tc-getCC) ${CFLAGS}" \
+			FC="$(tc-getFC)" \
+			LDR="$(tc-getFC)" \
+			FFLAGS="${FFLAGS}" )
+
+	einfo "Building Molden..."
+	emake -j1 "${args[@]}"
+	if use opengl ; then
+		einfo "Building Molden OpenGL helper..."
+		emake -j1 "${args[@]}" moldenogl
+	fi
+}
+
+src_install() {
+	dobin ${PN} g${PN}
+	if use opengl ; then
+		dobin ${PN}ogl
+	fi
+
+	dodoc HISTORY README REGISTER
+	cd doc
+	uncompress * && dodoc *
+}