New addition

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

5 files changed, 197 insertions, 0 deletions

diff --git a/sci-chemistry/aqua/ChangeLog b/sci-chemistry/aqua/ChangeLog
new file mode 100644
index 000000000000..7b66dabc7ec2
--- /dev/null
+++ b/sci-chemistry/aqua/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/aqua
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aqua/ChangeLog,v 1.1 2010/07/18 19:13:37 jlec Exp $
+
+*aqua-3.2 (18 Jul 2010)
+
+  18 Jul 2010; Justin Lecher <jlec@gentoo.org> +files/3.2-flags.patch,
+  +aqua-3.2.ebuild, +metadata.xml:
+  New addition
+
diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest
new file mode 100644
index 000000000000..255ed7f3470d
--- /dev/null
+++ b/sci-chemistry/aqua/Manifest
@@ -0,0 +1,15 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 3.2-flags.patch 4082 RMD160 7aea18ee558eab5458614058948c20def57dad28 SHA1 ed79bf1c643b1ade23c6e1d7a3c9e20edb9f5cca SHA256 3fe701b69bb174fd0c8c7b9227e5538947f82f78dfe47f534fba99cca8b284c1
+DIST aqua3.2.tar.gz 688408 RMD160 df72a47295f4c9509e9342241562a88458955eb5 SHA1 92c65374a8ba500fe493cb1752a81bfd857853ac SHA256 895291b1771f4db5b4a010ce797400a8c4d84095bf34d660dd3405223419242f
+EBUILD aqua-3.2.ebuild 1958 RMD160 d79dd096aa56875e8e683f27756142eb912c44d1 SHA1 ce45bab052a739022388a505e408719bf3295987 SHA256 d118beef83c16af795bbdb047861e61fa9fe7dbde18d02d5ab04ccf66b3c31ad
+MISC ChangeLog 354 RMD160 562b72733d41de16353a7a5919c9e8de4b1a22af SHA1 b934a558a93538e224307b1af95fa683d6930250 SHA256 df066d2958da6e1db00c0db90d19a2bbcd664285335192168b4160cceeeb9ba5
+MISC metadata.xml 226 RMD160 0355d90bd8d1c106a19b136045ebdf970a0a2485 SHA1 1db0b2a470657641079d6613829df49a5c043ed6 SHA256 094a3ac740c81b9afbff3c855ba93cc20a593cad2392f6f4404715608a836fa1
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.15 (GNU/Linux)
+
+iEYEARECAAYFAkxDUmYACgkQgAnW8HDreRacrQCgiGmnwZI9NoErrxPAH+Yf4EUr
+uskAoJS8avEL6mXvEhiNQ0XLI4RpkLBL
+=e1ds
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/aqua/aqua-3.2.ebuild b/sci-chemistry/aqua/aqua-3.2.ebuild
new file mode 100644
index 000000000000..6fb122b842e6
--- /dev/null
+++ b/sci-chemistry/aqua/aqua-3.2.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aqua/aqua-3.2.ebuild,v 1.1 2010/07/18 19:13:37 jlec Exp $
+
+EAPI="3"
+
+inherit eutils prefix 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"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="procheck"
+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 ${A} ->  ${DISTDIR}/aqua3.2.tar.gz."
+   if use doc; then
+      elog "nmr_manual.tar.gz  ->  ${DISTDIR}/${P}-nmr_manual.tar.gz"
+   fi
+}
+
+src_prepare() {
+	sed '1s:nwak:gawk:g' -i scripts/* || 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}" \
+		|| die
+	popd
+}
+
+src_install() {
+	rm -f scripts/conv* || die
+	dobin bin/* scripts/* || die
+	dosym AquaWhat /usr/bin/qwhat || die
+	dosym AquaHow /usr/bin/qhow || die
+	dosym AquaPseudo /usr/bin/qpseudo || die
+	dosym AquaDist /usr/bin/qdist || die
+	dosym AquaCalc /usr/bin/qcalc || die
+	dosym AquaAssign /usr/bin/qassign || die
+	dosym AquaRedun /usr/bin/qredun || die
+	dosym AquaCompl /usr/bin/qcompl || die
+
+	dodoc HISTORY HOW_TO_USE NEW README doc/* || die
+	dohtml html/* || die
+
+	insinto /usr/share/${PN}
+	doins data/* || die
+	if use examples; then
+		doins -r exmpls || die
+	fi
+
+	if use doc; then
+		dohtml -r manual || die
+	fi
+
+	cat >> "${T}"/34aqua <<- EOF
+	AQUADATADIR="${EPREFIX}/usr/share/${PN}"
+	EOF
+	doenvd "${T}"/34aqua || die
+}
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..dde7ca88a50f
--- /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>