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

6 files changed, 271 insertions, 0 deletions

diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest
new file mode 100644
index 000000000000..c50c49d67536
--- /dev/null
+++ b/sci-chemistry/procheck/Manifest
@@ -0,0 +1,3 @@
+DIST procheck-3.5.4-README 6585 SHA256 202d5b4d9ffaebdad19c368e6e6fd8ab54744c511609b1c609ef46c21fa0ffa0 SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a WHIRLPOOL 53a618978a9285e8a8f09c7ebd3e34951a8c1056c0894c1f4e4c11f73ad3127829322c9c7597fc6dea98f1fa4c40552e6caf383eed15aaeef0594cf93887d196
+DIST procheck-3.5.4-manual.tar.gz 517840 SHA256 3c2faa505be05102ccbe23473abdddc1cd4dc87c6b5e74222b7ea5c27b18db5a
+DIST procheck-3.5.4.tar.gz 522013 SHA256 4923fe5a7b86d5369fd639d0c77cfb866e574f076ec8c52424d746e843a404f4 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc WHIRLPOOL 2732981bdbb5269567019a645b401009bd48d782ab20b4f68bd213a90f7248a9fa3f46ab3a026aa0515a677a99826040d4c3f5464816ed4390b5091a6a98b375
diff --git a/sci-chemistry/procheck/files/3.5.4-ldflags.patch b/sci-chemistry/procheck/files/3.5.4-ldflags.patch
new file mode 100644
index 000000000000..453aebe3211f
--- /dev/null
+++ b/sci-chemistry/procheck/files/3.5.4-ldflags.patch
@@ -0,0 +1,49 @@
+diff --git a/Makefile b/Makefile
+index c5bb58f..0394b0a 100644
+--- a/Makefile
++++ b/Makefile
+@@ -35,31 +35,31 @@ distrib :
+ # Individual executables
+ # ----------------------
+ anglen : anglen.o
+-	$(F77) $(FOPTS) -o $@ anglen.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o
+ clean : clean.o
+-	$(F77) $(FOPTS) -o $@ clean.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o
+ rmsdev : rmsdev.o
+-	$(F77) $(FOPTS) -o $@ rmsdev.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o
+ secstr : secstr.o
+-	$(F77) $(FOPTS) -o $@ secstr.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o
+ gfac2pdb : gfac2pdb.o ps.o
+-	$(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o
+ pplot : pplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ pplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o
+ bplot : bplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ bplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o
+ tplot : tplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ tplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o
+ mplot : mplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ mplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o
+ vplot : vplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ vplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o
+ viol2pdb : viol2pdb.o ps.o
+-	$(F77) $(FOPTS) -o $@ viol2pdb.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o
+ wirplot : wirplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ wirplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o
+ nb : nb.c
+-	$(CC) $(COPTS) -o nb nb.c $(CLIBS)
++	$(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS)
+ 
+ # Individual rules for FORTRAN files with .inc files
+ # --------------------------------------------------
diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
new file mode 100644
index 000000000000..16a0658e654d
--- /dev/null
+++ b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
@@ -0,0 +1,35 @@
+diff --git a/pplot.f b/pplot.f
+index 7e06e68..c86b2b2 100644
+--- a/pplot.f
++++ b/pplot.f
+@@ -4720,6 +4720,7 @@ C---- Initialise variables
+           SCORE(IDIST) = 0.0
+  50   CONTINUE
+ 
++      REWIND(3)
+ C---- If the required residue is of a greater number than that required,
+ C     read through the file until come to it
+       IF (IRESID.GT.INRES) THEN
+diff --git a/ps.f b/ps.f
+index b652a7d..858b8e5 100644
+--- a/ps.f
++++ b/ps.f
+@@ -1705,12 +1705,14 @@ CVAX     -    CARRIAGECONTROL='LIST',
+ C---- If this is an existing file, then read through all its records until
+ C     get to the end of file
+       IF (.NOT.NEWFIL) THEN
++          CLOSE(14)
++          OPEN(14, file=fname, status='old', position='append', err=900)
+ 
+ C----     Loop through the file until reach the end
+- 100      CONTINUE
+-             READ(14,110,END=500) IREC
+- 110         FORMAT(A)
+-          GO TO 100
++C 100      CONTINUE
++C             READ(14,110,END=500) IREC
++C 110         FORMAT(A)
++C          GO TO 100
+ 
+ C---- If this is a new file, then write the header records to it
+       ELSE
\ No newline at end of file
diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml
new file mode 100644
index 000000000000..b3618ba38c1c
--- /dev/null
+++ b/sci-chemistry/procheck/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+    <name>Justin Lecher</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/procheck/procheck-3.5.4-r1.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r1.ebuild
new file mode 100644
index 000000000000..855c2badf4d0
--- /dev/null
+++ b/sci-chemistry/procheck/procheck-3.5.4-r1.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils fortran-2 multilib toolchain-funcs versionator
+
+DESCRIPTION="Checks the stereochemical quality of a protein structure"
+HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
+SRC_URI="
+	${P}.tar.gz ${P}-README
+	doc? ( ${P}-manual.tar.gz )"
+
+LICENSE="procheck"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE="doc"
+
+RDEPEND="app-shells/tcsh"
+DEPEND="${RDEPEND}"
+
+RESTRICT="fetch"
+
+S="${WORKDIR}/${PN}"
+
+pkg_nofetch() {
+	elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
+	elog "And follow the instruction for downloading."
+	elog "Files should be stored in following way"
+	elog "${PN}.tar.gz  ->  ${DISTDIR}/${P}.tar.gz"
+	elog "README  ->  ${DISTDIR}/${P}-README"
+	if use doc; then
+		elog "manual.tar.gz  ->  ${DISTDIR}/${P}-manual.tar.gz"
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-ldflags.patch
+}
+
+src_compile() {
+	emake \
+		F77=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		COPTS="${CFLAGS}" \
+		FOPTS="${FFLAGS}"
+}
+
+src_install() {
+	for i in *.scr; do
+		newbin ${i} ${i%.scr}
+	done
+
+	exeinto /usr/$(get_libdir)/${PN}/
+	doexe \
+		anglen \
+		clean \
+		rmsdev \
+		secstr \
+		gfac2pdb \
+		pplot \
+		bplot \
+		tplot \
+		mplot \
+		vplot \
+		viol2pdb \
+		wirplot \
+		nb
+	dodoc "${DISTDIR}"/${P}-README
+
+	insinto /usr/$(get_libdir)/${PN}/
+	doins *.dat *.prm
+	newins resdefs.dat resdefs.data
+
+	cat >> "${T}"/30${PN} <<- EOF
+	prodir="${EPREFIX}/usr/$(get_libdir)/${PN}/"
+	EOF
+
+	doenvd "${T}"/30${PN}
+
+	if use doc; then
+		pushd "${WORKDIR}"
+			dohtml -r manual
+		popd
+	fi
+}
diff --git a/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild
new file mode 100644
index 000000000000..0c4683e03a72
--- /dev/null
+++ b/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild
@@ -0,0 +1,88 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils fortran-2 multilib toolchain-funcs versionator
+
+DESCRIPTION="Checks the stereochemical quality of a protein structure"
+HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
+SRC_URI="
+	${P}.tar.gz ${P}-README
+	doc? ( ${P}-manual.tar.gz )"
+
+LICENSE="procheck"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc"
+
+RDEPEND="app-shells/tcsh"
+DEPEND="${RDEPEND}"
+
+RESTRICT="fetch"
+
+S="${WORKDIR}/${PN}"
+
+pkg_nofetch() {
+	elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
+	elog "And follow the instruction for downloading."
+	elog "Files should be stored in following way"
+	elog "${PN}.tar.gz  ->  ${DISTDIR}/${P}.tar.gz"
+	elog "README  ->  ${DISTDIR}/${P}-README"
+	use doc && elog "manual.tar.gz  ->  ${DISTDIR}/${P}-manual.tar.gz"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-ldflags.patch \
+		"${FILESDIR}"/${P}-close.patch
+}
+
+src_compile() {
+	emake \
+		F77=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		COPTS="${CFLAGS}" \
+		FOPTS="${FFLAGS} -std=legacy"
+}
+
+src_install() {
+	for i in *.scr; do
+		newbin ${i} ${i%.scr}
+	done
+
+	exeinto /usr/libexec/${PN}/
+	doexe \
+		anglen \
+		clean \
+		rmsdev \
+		secstr \
+		gfac2pdb \
+		pplot \
+		bplot \
+		tplot \
+		mplot \
+		vplot \
+		viol2pdb \
+		wirplot \
+		nb
+	dodoc "${DISTDIR}"/${P}-README
+
+	insinto /usr/libexec/${PN}/
+	doins *.dat *.prm
+	newins resdefs.dat resdefs.data
+
+	cat >> "${T}"/30${PN} <<- EOF
+	prodir="${EPREFIX}/usr/libexec/${PN}/"
+	EOF
+
+	doenvd "${T}"/30${PN}
+
+	if use doc; then
+		pushd "${WORKDIR}" > /dev/null
+			docinto html
+			dodoc -r manual
+		popd > /dev/null
+	fi
+}