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

4 files changed, 187 insertions, 0 deletions

diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest
new file mode 100644
index 000000000000..7f6594d70fe4
--- /dev/null
+++ b/sci-chemistry/aqua/Manifest
@@ -0,0 +1,2 @@
+DIST aqua-3.2-nmr_manual.tar.gz 632031 SHA256 89bbc2501831e547fec2fe755bbc0081f672e5e2c7adb83618699e6825f73996
+DIST aqua3.2.tar.gz 688408 SHA256 895291b1771f4db5b4a010ce797400a8c4d84095bf34d660dd3405223419242f
diff --git a/sci-chemistry/aqua/aqua-3.2-r2.ebuild b/sci-chemistry/aqua/aqua-3.2-r2.ebuild
new file mode 100644
index 000000000000..74fccddc5dd2
--- /dev/null
+++ b/sci-chemistry/aqua/aqua-3.2-r2.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="Program suite in this distribution calculates restraint violations"
+HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
+SRC_URI="
+	${PN}${PV}.tar.gz
+	doc? ( ${P}-nmr_manual.tar.gz )"
+
+SLOT="0"
+LICENSE="procheck"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc examples"
+
+RDEPEND="sci-chemistry/procheck"
+DEPEND=""
+
+RESTRICT="fetch"
+
+S="${WORKDIR}"/${PN}${PV}
+
+pkg_nofetch() {
+	elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
+	elog "And follow the instruction for downloading ${PN}${PV}.tar.gz ->  ${DISTDIR}/${PN}${PV}.tar.gz."
+	if use doc; then
+		elog "nmr_manual.tar.gz  ->  ${DISTDIR}/${P}-nmr_manual.tar.gz"
+	fi
+}
+
+src_prepare() {
+	sed \
+		-e 's:nawk:gawk:g' \
+		-e "s:/bin/gawk:${EPREFIX}/usr/bin/gawk:g" \
+		-e "s:/usr/local/bin/perl:${EPREFIX}/usr/bin/perl:g" \
+		-i $(find . -type f) || die
+	epatch "${FILESDIR}"/${PV}-flags.patch
+}
+
+src_compile() {
+	pushd src > /dev/null
+	emake \
+		MYROOT="${WORKDIR}" \
+		CC="$(tc-getCC)" \
+		FC="$(tc-getFC)" \
+		CFLAGS="${CFLAGS} -I../sub/lib" \
+		FFLAGS="${FFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		exth
+	emake \
+		MYROOT="${WORKDIR}" \
+		CC="$(tc-getCC)" \
+		FC="$(tc-getFC)" \
+		CFLAGS="${CFLAGS} -I../sub/lib" \
+		FFLAGS="${FFLAGS}" \
+		LDFLAGS="${LDFLAGS}"
+	popd
+}
+
+src_install() {
+	rm -f scripts/conv* || die
+	dobin bin/* scripts/*
+	dosym AquaWhat /usr/bin/qwhat
+	dosym AquaHow /usr/bin/qhow
+	dosym AquaPseudo /usr/bin/qpseudo
+	dosym AquaDist /usr/bin/qdist
+	dosym AquaCalc /usr/bin/qcalc
+	dosym AquaAssign /usr/bin/qassign
+	dosym AquaRedun /usr/bin/qredun
+	dosym AquaCompl /usr/bin/qcompl
+
+	dodoc HISTORY HOW_TO_USE NEW README doc/*
+	dohtml html/*
+
+	insinto /usr/share/${PN}
+	doins data/*
+	if use examples; then
+		doins -r exmpls
+	fi
+
+	if use doc; then
+		dohtml -r manual
+	fi
+
+	cat >> "${T}"/34aqua <<- EOF
+	AQUADATADIR="${EPREFIX}/usr/share/${PN}"
+	EOF
+	doenvd "${T}"/34aqua
+}
diff --git a/sci-chemistry/aqua/files/3.2-flags.patch b/sci-chemistry/aqua/files/3.2-flags.patch
new file mode 100644
index 000000000000..cd12fbb9a324
--- /dev/null
+++ b/sci-chemistry/aqua/files/3.2-flags.patch
@@ -0,0 +1,84 @@
+diff --git a/src/makefile b/src/makefile
+index 3113471..dd7a320 100644
+--- a/src/makefile
++++ b/src/makefile
+@@ -176,47 +176,46 @@ nrutil.h:
+ # Executable files
+ 
+ $(BIN)/AquaWhat:    AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS)
+-	$(CC) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) $(LDFLAGS)
++	$(CC) $(LDFLAGS) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS)
+ 
+ $(BIN)/AquaHow:	    AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS)
+-	$(CC) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
++	$(CC) $(LDFLAGS) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS)
+ 
+ $(BIN)/AquaPseudo:  AquaPseudo.o $(OBJECTS) $(R_OBJECTS) 
+-	$(CC) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) $(LDFLAGS)
++	$(CC) $(LDFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS)
+ 
+ $(BIN)/AquaDist:    AquaDist.o $(OBJECTS) 
+-	$(CC) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) $(LDFLAGS) -lm
++	$(CC) $(LDFLAGS) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) -lm
+ 
+ $(BIN)/AquaCalc:    AquaCalc.o $(OBJECTS) $(RNG_OBJECTS)
+-	$(CC) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) -lm
++	$(CC) $(LDFLAGS) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -lm
+ 
+ $(BIN)/AquaAssign:  AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
+-	$(CC) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
++	$(CC) $(LDFLAGS) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
+ 
+ $(BIN)/AquaCompl:  AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) 
+-	$(CC) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -lm  
++	$(CC) $(LDFLAGS) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -lm  
+ 
+ $(BIN)/AquaRedun:  AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) 
+-	$(CC) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
++	$(CC) $(LDFLAGS) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
+ 
+ $(BIN)/testnew:	    testnew.o $(OBJECTS)
+-	$(CC) -o $(BIN)/testnew testnew.o $(OBJECTS) $(LDFLAGS)
++	$(CC) $(LDFLAGS) -o $(BIN)/testnew testnew.o $(OBJECTS)
+ 
+ $(BIN)/getproj:    getproj.c 
+-	$(CC) -o $(BIN)/getproj -O getproj.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BIN)/getproj getproj.c
+ 
+ $(BIN)/AquaPlot:    AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
+-	$(CC) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS)
++	$(CC) $(LDFLAGS) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
+ 
+ $(BIN)/Qext:	   Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
+-	$(CC) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS)
++	$(CC) $(LDFLAGS) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
+ 
+ $(BIN)/StarTest:	StarTest.o
+-	$(CC) -o $(BIN)/StarTest StarTest.o $(LDFLAGS) $(STARFLAGS) $(STARLIBS)
++	$(CC) $(LDFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS)
+ 
+ exth:		exth.f
+-	f77 -o exth -O2 exth.f
+-	strip exth
++	$(FC) $(FFLAGS) -o exth -O2 exth.f
+ 
+ 
+ # Object files
+@@ -269,7 +268,7 @@ AquaCommon.o:	AquaCommon.c AquaCommon.h nrutil.h \
+ 	$(CC) -c AquaCommon.c $(CFLAGS)
+ 
+ nrutil.o:	nrutil.c nrutil.h
+-	$(CC) -c nrutil.c -DANSI
++	$(CC) $(CFLAGS) -c nrutil.c -DANSI
+ 
+ AquaFuncts.o:	AquaFuncts.c AquaFuncts.h AquaFuncts_cv.h AquaFuncts_io.h\
+ 		AquaStrucset.h AquaFiles.h\
+@@ -319,7 +318,7 @@ $(LIB)/MenuFuncts.o:	$(LIB)/MenuFuncts.c $(LIB)/MenuTypes.h $(LIB)/MenuFuncts.h\
+ 	cd $(LIB); $(CC) -c MenuFuncts.c $(CFLAGS)
+ 
+ cv_subs.o:	cv_subs.f
+-	f77 -c cv_subs.f $(FFLAGS)
++	$(FC) -c cv_subs.f $(FFLAGS)
+ 
+ Qext.o:		Qext.c Qext.h\
+ 		$(LIB)/MenuFuncts.h $(LIB)/Functs.h $(G_HEADERS)
diff --git a/sci-chemistry/aqua/metadata.xml b/sci-chemistry/aqua/metadata.xml
new file mode 100644
index 000000000000..1837bbc07a6e
--- /dev/null
+++ b/sci-chemistry/aqua/metadata.xml
@@ -0,0 +1,8 @@
+<?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>
+	</maintainer>
+</pkgmetadata>