reinit the tree, so we can have metadata

4 files changed, 194 insertions, 0 deletions

diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest
new file mode 100644
index 000000000000..0a70a95426cb
--- /dev/null
+++ b/sci-chemistry/aqua/Manifest
@@ -0,0 +1,7 @@
+AUX aqua-3.2-flags.patch 4211 SHA256 dab0b840c6425d0295727224e5ef7ba9f48a4c013d45d24a141c46684e0d8eee SHA512 059cea5403fb4cb01b0fcd4d2a2fe4b4aea725e9362a6188ccd3756ced35e324cda5efb21d3ad2a95a842e9d83f8e728a16b36e4b6a479ae32da8816d7eafdfc WHIRLPOOL b1c2f4eff77458cb662b3aadc1c3f065cb2a7fb6c01bb3a2f41ce8a66b9d4c5153aff228b0e29a707d9a75cdef3f253572ba8479b0d3c26ddc812f72c6247b03
+DIST aqua-3.2-nmr_manual.tar.gz 632031 SHA256 89bbc2501831e547fec2fe755bbc0081f672e5e2c7adb83618699e6825f73996 SHA512 9b125b03507afebf15301c893efffae9be4e9695b9c577e5c2a80e83b620d04b4c27e867adf06336afa1556eddc96aa97de936028e503b1e85e156542664da0f WHIRLPOOL 181d320edd32faaac71a48163975ab6899221d7c85744eedfb8954d3360c974a0c8223b8b0f00375e2369fa7350df2e16a1062698be01c625ef00308a8ee0887
+DIST aqua3.2.tar.gz 688408 SHA256 895291b1771f4db5b4a010ce797400a8c4d84095bf34d660dd3405223419242f SHA512 1939f662a68122da613368aa106d7a31525903014420035eba9d10c3bd99b04d654d156328d308673003854233a02c1da48c036f3187fa1f0f303cc5928edd6a WHIRLPOOL 458fc0e574273fd9d2647ef8b2788c98669c9f96133f7132eddc9cbfb981e42894f5e4fd0e8d67f52ddb4c6424399b21973d4d87a175b440d81b7b955fe3fe41
+EBUILD aqua-3.2-r3.ebuild 2071 SHA256 2358cf9bc664f64e3e832c99c0f8aba97141a1ece67263abd97c58ec09be9b28 SHA512 4135a83c758759697fba718388473dfbc6893844db980b19174fe167a9e029aa273a04b04376404cf6a88378dda3e2ac7c2f8f3f526b75765f7f2abd054b802c WHIRLPOOL 238820a9d5a409006a6629c66fb3e7089cc630a1cf43c6e7ed76951fe955b5c96e657186aa92668b0b7b652e290bf5fef1867635f25dcb600c413991ba4478a8
+MISC ChangeLog 2589 SHA256 6a4cefc3a06bf04f71dee23fc72f450f8ff1723b214a7d92745fdf8a7e2cd20e SHA512 975a6f59950625b119248a1f0704ad3d2fb060ea776ac731481cb919b6198fdeadef8840008d4f1c1b5105292f9b708720a4519aa7a95701a244bb1f3581da74 WHIRLPOOL 1d228388d85f96d4bf7fb0416e03f12129d02457f2e52a2933dc96f37143995c219001f491ae85711474bbd22c7c767125728ba710b0a1eed25a5744d609cdec
+MISC ChangeLog-2015 1234 SHA256 2e29785d9cd11da6615c45c9a7c47c077c19cefa07b670f0a0167712efdc6b59 SHA512 36243b25e872810d330f05bc488572a1fe334f7b20c0e3b7cd61404647d10f55076b5a55d39dfe353cf65053ae2feefe6b9f8137dc04475b42c0bb5a4c73ac0f WHIRLPOOL c87e94c566d0b2247afb1f7a0a24dee565c5908a67e3fc4726383a0db9baa32655af58e57665f25b1950c31ba77eefc70e7ba901a45792d6943c08b524d69bc2
+MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d
diff --git a/sci-chemistry/aqua/aqua-3.2-r3.ebuild b/sci-chemistry/aqua/aqua-3.2-r3.ebuild
new file mode 100644
index 000000000000..74e4e60416f7
--- /dev/null
+++ b/sci-chemistry/aqua/aqua-3.2-r3.ebuild
@@ -0,0 +1,95 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit 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? ( ${P}-nmr_manual.tar.gz )"
+
+SLOT="0"
+LICENSE="procheck"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc examples"
+
+RDEPEND="sci-chemistry/procheck"
+DEPEND="app-shells/tcsh"
+
+RESTRICT="fetch"
+
+S="${WORKDIR}"/${PN}${PV}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-flags.patch
+)
+
+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 $(find . -type f) || die
+	default
+}
+
+src_compile() {
+	cd src || die
+	emake \
+		MYROOT="${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="${LDFLAGS}"
+}
+
+src_install() {
+	rm -f scripts/conv* || die
+	dobin bin/* scripts/*
+	dosym AquaWhat /usr/bin/qwhat
+	dosym AquaHow /usr/bin/qhow
+	dosym AquaPseudo /usr/bin/qpseudo
+	dosym AquaDist /usr/bin/qdist
+	dosym AquaCalc /usr/bin/qcalc
+	dosym AquaAssign /usr/bin/qassign
+	dosym AquaRedun /usr/bin/qredun
+	dosym AquaCompl /usr/bin/qcompl
+
+	dodoc HISTORY HOW_TO_USE NEW README doc/*
+	dohtml html/*
+
+	insinto /usr/share/${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/aqua-3.2-flags.patch b/sci-chemistry/aqua/files/aqua-3.2-flags.patch
new file mode 100644
index 000000000000..a60841b8ce08
--- /dev/null
+++ b/sci-chemistry/aqua/files/aqua-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) $(CFLAGS) -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) $(CFLAGS) -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) $(CFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS)
+ 
+ $(BIN)/AquaDist:    AquaDist.o $(OBJECTS) 
+-	$(CC) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) $(LDFLAGS) -lm
++	$(CC) $(LDFLAGS) $(CFLAGS) -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) $(CFLAGS) -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) $(CFLAGS) -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) $(CFLAGS) -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) $(CFLAGS) -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) $(CFLAGS) -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) $(CFLAGS) -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) $(CFLAGS) -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) $(CFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS)
+ 
+ exth:		exth.f
+-	f77 -o exth -O2 exth.f
+-	strip exth
++	$(FC) $(FFLAGS) $(LDFLAGS) -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..da36ecbfcd6a
--- /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>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+</pkgmetadata>