Fixes for upstreams changes

Package-Manager: portage-2.2.0_alpha6/cvs/Linux x86_64

4 files changed, 60 insertions, 18 deletions

diff --git a/sci-chemistry/tinker/ChangeLog b/sci-chemistry/tinker/ChangeLog
index 2d762b973d8c..cb98628bbdbf 100644
--- a/sci-chemistry/tinker/ChangeLog
+++ b/sci-chemistry/tinker/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/tinker
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/ChangeLog,v 1.27 2010/12/02 10:51:37 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/ChangeLog,v 1.28 2010/12/02 22:15:37 jlec Exp $
+
+*tinker-6 (02 Dec 2010)
+
+  02 Dec 2010; Justin Lecher <jlec@gentoo.org> +files/6-openmp.patch,
+  +tinker-6.ebuild, -tinker-6.0.ebuild:
+  Fixes for upstreams changes
 
   02 Dec 2010; Justin Lecher <jlec@gentoo.org> tinker-5.1.09.ebuild,
   tinker-6.0.ebuild:
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
index 9d3cd550494c..c0edd1218b61 100644
--- a/sci-chemistry/tinker/Manifest
+++ b/sci-chemistry/tinker/Manifest
@@ -2,16 +2,17 @@
 Hash: SHA1
 
 AUX 5.1.09-Makefile.patch 319 RMD160 67b2e42fabfea415ba0933f074f99b69804ab451 SHA1 4e86541e3b5b6544ea7be48bf4453013b8f29b7e SHA256 8273ad63e02dec2b286f29289d41a86b1cc750b3d705ac69eeaf0dd890b887de
+AUX 6-openmp.patch 396 RMD160 9638f6347cde47c5206ffa440fa177c3652156a9 SHA1 123e50a224316e2144b4f6dd27d57351f3737202 SHA256 5818373bbac86ee9d7bacbbca029cb33a66df017c36d9363a12f5cbfa2cd8a01
 DIST tinker-5.1.09.tar.gz 14071638 RMD160 9f20036d9e483c89fe516db8bf4a0195d15b79bf SHA1 71f4b1c0d1f6ef5bcb47de2145fab9885f6f3641 SHA256 61765adfe260e3f3083243542dac49d38141191d5d6580e9a66a29c31d5a3183
-DIST tinker-6.0.tar.gz 18171344 RMD160 45143abcd9e94846027d74b5c2a1dde25e4143ad SHA1 c1209e2076bea75a9201168f57b6b53710a5397b SHA256 33269db000dd25fe8a059bfd9bd2bc8e51e4b34ae568bd4da7ee8c355e042029
+DIST tinker-6.tar.gz 18475753 RMD160 c236c01f868119c8fdf9e25f9dc63f51fd8a21fa SHA1 5bda1b5aa78e101108b807b78166fef2157908e5 SHA256 f3962cf39df1ccfb2a425837add7de58cda3e21adebbe1141fee6e3869ba5fc0
 EBUILD tinker-5.1.09.ebuild 1917 RMD160 0fd33d1567ef278b7b54fd9cdab35aabd94ae005 SHA1 fe58901fb8dfa7afe55b5b03c0a7da69d62ef40e SHA256 c6811cbfb4a1669f5699afdb7ebcc1cc792012b797c6d5551ba43ae97aa14adc
-EBUILD tinker-6.0.ebuild 1832 RMD160 f572ceb3a9012cef7fb60722d5dbb9810bf9f350 SHA1 e94c7f85552b282cb40860a06beed1c843ec3e90 SHA256 928daa428bb3b3b9266b6c707f212cd149654ef77e9ad669e0141001fdc70a4b
-MISC ChangeLog 4189 RMD160 13c6aaf221d47d692cd67da81a91f83909f824cb SHA1 7e43eb3dfb71bbb7295db0bd425c9d0cfa026df2 SHA256 5b6d04109080ada029dda5e02487f4e4cb8ef23ddf4065c9f1a44c8ff41e0dc7
+EBUILD tinker-6.ebuild 2428 RMD160 d76233854c6629e642bb66333f7909a65cea36c9 SHA1 e521c8f9546119658cd81c0f15814d2e48cf9d76 SHA256 8a37a865e36c872de9cfc3381500598039c903e485e865cf8ae14fdad4015937
+MISC ChangeLog 4355 RMD160 a1e575114fa57a05ea37be2dbe00b3997d47019a SHA1 12418c865720a64458e487e1eab089aba3ec1c3d SHA256 9d5ae775c8d4c983c03f86842ef7f268f920d14c4f3cf097e133982de9109fbb
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
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-R6IAn0WJ64iXmFtN6YRQaTq4AqcwYXV3
-=dxow
+iEYEARECAAYFAkz4GpAACgkQgAnW8HDreRafVQCfUWt+pS0JJkUSRbAU1xaIB4GT
+LkAAn0efJKK2sEEiwj+j5casEYZX+JCJ
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diff --git a/sci-chemistry/tinker/files/6-openmp.patch b/sci-chemistry/tinker/files/6-openmp.patch
new file mode 100644
index 000000000000..3666fbd0bfc4
--- /dev/null
+++ b/sci-chemistry/tinker/files/6-openmp.patch
@@ -0,0 +1,15 @@
+diff --git a/source/initial.f b/source/initial.f
+index 835f228..4099c74 100644
+--- a/source/initial.f
++++ b/source/initial.f
+@@ -73,8 +73,8 @@ c
+ c
+ c     Intel compiler extensions to OpenMP standard
+ c
+-!$    call kmp_set_stacksize (2**30)
+-!$    call kmp_set_blocktime (0)
++!    call kmp_set_stacksize (2**30)
++!    call kmp_set_blocktime (0)
+ c
+ c     values of machine precision constants
+ c
diff --git a/sci-chemistry/tinker/tinker-6.0.ebuild b/sci-chemistry/tinker/tinker-6.ebuild
index 92d1725a5f44..687335483ebc 100644
--- a/sci-chemistry/tinker/tinker-6.0.ebuild
+++ b/sci-chemistry/tinker/tinker-6.ebuild
@@ -1,11 +1,11 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/tinker-6.0.ebuild,v 1.5 2010/12/02 10:51:39 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/tinker-6.ebuild,v 1.1 2010/12/02 22:15:39 jlec Exp $
 
 EAPI="2"
 FORTRAN="gfortran ifc"
 
-inherit fortran java-pkg-opt-2 toolchain-funcs
+inherit fortran flag-o-matic java-pkg-opt-2 toolchain-funcs
 
 DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM"
 HOMEPAGE="http://dasher.wustl.edu/tinker/"
@@ -18,16 +18,23 @@ IUSE="examples"
 
 DEPEND=">=virtual/jdk-1.6"
 RDEPEND="
+	>=sci-libs/fftw-3.2.2-r1[fortran,threads]
 	dev-libs/maloc
 	!dev-util/diffuse
 	>=virtual/jre-1.6"
 RESTRICT="mirror"
 
-S="${WORKDIR}"/tinker/source
+S="${WORKDIR}"/${PN}${PV}/source
 
 pkg_setup() {
 	fortran_pkg_setup
 	java-pkg-opt-2_pkg_setup
+	tc-has-openmp || die "Please use an openmp capable compiler like gcc[openmp]"
+}
+
+src_prepare() {
+	sed 's:strip:true:g' -i ../make/Makefile
+	[[ ${FORTRANC} == "ifc" ]] || epatch "${FILESDIR}"/${PV}-openmp.patch
 }
 
 src_compile() {
@@ -36,6 +43,19 @@ src_compile() {
 		[[ -f ${i}/libjvm.so ]] && javalib=${i}
 	done
 
+	# use dummy routines in pmpb.f instead of apbs calls
+	rm pmpb.c || die
+
+	if [[ ${FORTRANC} == "gfortran" ]]; then
+		append-flags -fopenmp
+		_omplib="-lgomp"
+	else
+		append-flags -openmp
+		_omplib="-liomp5"
+	fi
+
+	_fftwlib="$(pkg-config --libs fftw3 fftw3_threads)"
+
 	emake \
 		-f ../make/Makefile \
 		F77="${FORTRANC}" \
@@ -44,8 +64,8 @@ src_compile() {
 		OPTFLAGS="${FFLAGS}" \
 		LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \
 		INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \
-		LIBS="-lmaloc -L${javalib} -ljvm" \
-		|| die
+		LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \
+		all || die
 
 	mkdir "${S}"/../bin || die
 
@@ -56,7 +76,7 @@ src_compile() {
 }
 
 src_test() {
-	cd "${WORKDIR}"/tinker/test/
+	cd "${WORKDIR}"/${PN}${PV}/test/
 	for test in *.run; do
 		einfo "Testing ${test} ..."
 		bash ${test} || die
@@ -64,19 +84,19 @@ src_test() {
 }
 
 src_install() {
-	dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/* || die
+	dobin "${WORKDIR}"/${PN}${PV}/perl/mdavg "${WORKDIR}"/${PN}${PV}/bin/* || die
 
 	insinto /usr/share/${PN}/
-	doins -r "${WORKDIR}"/${PN}/params || die
+	doins -r "${WORKDIR}"/${PN}${PV}/params || die
 
 	dodoc \
-		"${WORKDIR}"/${PN}/doc/{*.txt,announce/release-*,*.pdf,0README} || die
+		"${WORKDIR}"/${PN}${PV}/doc/{*.txt,announce/release-*,*.pdf,0README} || die
 
 	if use examples; then
 		insinto /usr/share/${P}
-		doins -r "${WORKDIR}"/${PN}/example || die
+		doins -r "${WORKDIR}"/${PN}${PV}/example || die
 
-		doins -r "${WORKDIR}"/${PN}/test || die
+		doins -r "${WORKDIR}"/${PN}${PV}/test || die
 	fi
 
 }