[gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/

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* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-03-07  1:49 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-03-07  1:49 UTC (permalink / raw
  To: gentoo-commits

commit:     cc628857ec107cbf152b1061d11322fd80d2a83d
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 01:48:51 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 01:48:51 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cc628857

[sci-chemistry/ambertools] now it should work

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.4.ebuild |   24 ++++++++++++++++++++++++
 1 files changed, 24 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index 6d22631..aea832a 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -98,3 +98,27 @@ src_compile() {
 	cd AmberTools/src
 	emake || die
 }
+
+src_install() {
+	for x in bin/*
+		do dobin $x || die
+	done
+	rm "${ED}/usr/bin/yacc"
+	sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
+		-i "${ED}/usr/bin/xleap" \
+		-i "${ED}/usr/bin/tleap" || die
+	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
+	dolib.a lib/*
+	insinto /usr/include/${PN}
+	doins include/*
+	insinto /usr/share/${PN}
+	doins -r dat
+	cd AmberTools
+	doins -r benchmarks
+	doins -r examples
+	doins -r test
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr"
+	EOF
+	doenvd "${T}"/ambertools
+}



^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-03-07  1:49 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-03-07  1:49 UTC (permalink / raw
  To: gentoo-commits

commit:     69d60a43ed6fba2d70f6fc646121455475c7399f
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 01:20:28 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 01:20:28 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=69d60a43

[sci-chemistry/ambertools] Now it compiles =D

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.4.ebuild |   10 ++++++++--
 1 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index d5fb35b..6d22631 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -71,7 +71,13 @@ src_configure() {
 		-e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=$(pkg-config netcdf --libs):g" \
 		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
 		-e "s:-O3::g" \
-		-i configure
+		-i configure || die
+	sed -e "s:arsecond_:arscnd_:g" \
+		-i sff/time.c \
+		-i sff/sff.h \
+		-i sff/sff.c || die
+	sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \
+		-i nss/Makefile || die
 
 	local myconf
 
@@ -90,5 +96,5 @@ src_configure() {
 
 src_compile() {
 	cd AmberTools/src
-	emake -f Makefile || die
+	emake || die
 }



^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-03-07  1:55 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-03-07  1:55 UTC (permalink / raw
  To: gentoo-commits

commit:     23dce32e9c9b18d3fd4d684fe90ba1c8983b0eb5
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 01:55:03 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 01:55:03 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=23dce32e

Fix typo

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.4.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index aea832a..e4e58ab 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -120,5 +120,5 @@ src_install() {
 	cat >> "${T}"/99ambertools <<- EOF
 	AMBERHOME="${EPREFIX}/usr"
 	EOF
-	doenvd "${T}"/ambertools
+	doenvd "${T}"/99ambertools
 }



^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-03-07 18:20 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-03-07 18:20 UTC (permalink / raw
  To: gentoo-commits

commit:     f9b1513cec8e708df540402c8f0826809f04aa37
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 18:18:51 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 18:20:22 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f9b1513c

[sci-chemistry/ambertools] Fix issues with path

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.4.ebuild |   16 ++++++++++++----
 1 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index e4e58ab..06fa85a 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -104,9 +104,17 @@ src_install() {
 		do dobin $x || die
 	done
 	rm "${ED}/usr/bin/yacc"
-	sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
-		-i "${ED}/usr/bin/xleap" \
-		-i "${ED}/usr/bin/tleap" || die
+	dobin AmberTools/src/antechamber/mopac.sh
+	sed -e "s:bin/mopac:bin/mopac7:g" \
+		-i "${ED}/bin/mopac.sh" || die
+	# Make symlinks untill binpath for amber will be fixed
+	dodir /usr/share/${PN}/bin
+	for x in "${ED}"/usr/bin/*
+		do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
+	done
+#	sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
+#		-i "${ED}/usr/bin/xleap" \
+#		-i "${ED}/usr/bin/tleap" || die
 	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
 	dolib.a lib/*
 	insinto /usr/include/${PN}
@@ -118,7 +126,7 @@ src_install() {
 	doins -r examples
 	doins -r test
 	cat >> "${T}"/99ambertools <<- EOF
-	AMBERHOME="${EPREFIX}/usr"
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
 	EOF
 	doenvd "${T}"/99ambertools
 }



^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-03-07 18:20 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-03-07 18:20 UTC (permalink / raw
  To: gentoo-commits

commit:     cd781ace2f722cdc9038a44f3247737eaa82f4cd
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 18:20:02 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 18:20:22 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cd781ace

[sci-chemistry/ambertools] Fix typo

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.4.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index 06fa85a..ec09ed4 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -105,7 +105,7 @@ src_install() {
 	done
 	rm "${ED}/usr/bin/yacc"
 	dobin AmberTools/src/antechamber/mopac.sh
-	sed -e "s:bin/mopac:bin/mopac7:g" \
+	sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
 		-i "${ED}/bin/mopac.sh" || die
 	# Make symlinks untill binpath for amber will be fixed
 	dodir /usr/share/${PN}/bin



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* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-03-07 18:23 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-03-07 18:23 UTC (permalink / raw
  To: gentoo-commits

commit:     fe218c4b2690fe172197f68fa04c226ae1296330
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 18:22:51 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 18:22:51 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fe218c4b

Fix another typo

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.4.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index ec09ed4..76f17ef 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -106,7 +106,7 @@ src_install() {
 	rm "${ED}/usr/bin/yacc"
 	dobin AmberTools/src/antechamber/mopac.sh
 	sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
-		-i "${ED}/bin/mopac.sh" || die
+		-i "${ED}/usr/bin/mopac.sh" || die
 	# Make symlinks untill binpath for amber will be fixed
 	dodir /usr/share/${PN}/bin
 	for x in "${ED}"/usr/bin/*



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* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-03-07 18:28 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-03-07 18:28 UTC (permalink / raw
  To: gentoo-commits

commit:     2dae7262cde708e8782544a591ed4e90798366a3
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 18:28:02 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 18:28:02 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2dae7262

Fix another typo with symlinks

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.4.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index 76f17ef..8b39b57 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -109,7 +109,7 @@ src_install() {
 		-i "${ED}/usr/bin/mopac.sh" || die
 	# Make symlinks untill binpath for amber will be fixed
 	dodir /usr/share/${PN}/bin
-	for x in "${ED}"/usr/bin/*
+	for x in $(ls "${ED}"/usr/bin/*)
 		do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
 	done
 #	sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \



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* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-03-07 18:34 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-03-07 18:34 UTC (permalink / raw
  To: gentoo-commits

commit:     413c37ea8bd927e362952b102cb9d951f662350a
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 18:34:26 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 18:34:26 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=413c37ea

Fix another typo with symlinks

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.4.ebuild |    6 ++++--
 1 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index 8b39b57..9e1297e 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -101,7 +101,7 @@ src_compile() {
 
 src_install() {
 	for x in bin/*
-		do dobin $x || die
+		do dobin ${x} || die
 	done
 	rm "${ED}/usr/bin/yacc"
 	dobin AmberTools/src/antechamber/mopac.sh
@@ -109,9 +109,11 @@ src_install() {
 		-i "${ED}/usr/bin/mopac.sh" || die
 	# Make symlinks untill binpath for amber will be fixed
 	dodir /usr/share/${PN}/bin
-	for x in $(ls "${ED}"/usr/bin/*)
+	cd "${ED}/usr/bin"
+	for x in *
 		do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
 	done
+	cd "${S}"
 #	sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
 #		-i "${ED}/usr/bin/xleap" \
 #		-i "${ED}/usr/bin/tleap" || die



^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-03-15 10:23 Justin Lecher
  0 siblings, 0 replies; 19+ messages in thread
From: Justin Lecher @ 2011-03-15 10:23 UTC (permalink / raw
  To: gentoo-commits

commit:     a29f1f371cd826e6733dceac660de3651c4b7683
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 15 10:21:33 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 15 10:21:33 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a29f1f37

Ignore fatal patch size

(Portage version: 2.2.0_alpha27/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/ambertools/ChangeLog             |   10 ++++++++++
 sci-chemistry/ambertools/ambertools-1.4.ebuild |    7 ++-----
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
new file mode 100644
index 0000000..9c558c3
--- /dev/null
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/ambertools
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  15 Mar 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild:
+  Remove fortran.eclass
+
+  14 Mar 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild:
+  Remove fortran.eclass removal
+

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index fda14ee..9e0e96b 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -4,9 +4,7 @@
 
 EAPI="4"
 
-inherit toolchain-funcs eutils fortran
-
-FORTRAN="g77 gfortran ifc"
+inherit toolchain-funcs eutils
 
 DESCRIPTION="A suite of programs for carrying out complete molecular mechanics investigations"
 HOMEPAGE="http://ambermd.org/#AmberTools"
@@ -38,7 +36,6 @@ pkg_nofetch() {
 }
 
 pkg_setup() {
-	need_fortran "${FORTRAN}"
 	if use openmp &&
 	[[ $(tc-getCC)$ == *gcc* ]] &&
 		( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
@@ -68,7 +65,7 @@ src_configure() {
 		-e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
 		-e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
 		-e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \
-		-e "s:fc=g77:fc=${FORTRANC}:g" \
+		-e "s:fc=g77:fc=$(tc-getFC):g" \
 		-e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=$(pkg-config netcdf --libs):g" \
 		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
 		-e "s:-O3::g" \



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* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-06-21 11:54 Justin Lecher
  0 siblings, 0 replies; 19+ messages in thread
From: Justin Lecher @ 2011-06-21 11:54 UTC (permalink / raw
  To: gentoo-commits

commit:     8436ce9d0b5b4908c7588716acf111347bdf4e81
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 21 10:50:20 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 21 10:50:20 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8436ce9d

commit

(Portage version: 2.2.0_alpha41/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/ambertools/ChangeLog             |    4 ++++
 sci-chemistry/ambertools/ambertools-1.4.ebuild |   24 +++++++++++-------------
 sci-chemistry/ambertools/ambertools-1.5.ebuild |   24 +++++++++++-------------
 3 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index 26101af..ea945fd 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild,
+  ambertools-1.5.ebuild:
+  Added fortran-2.eclass support
+
 *ambertools-1.5 (04 Jun 2011)
 
   04 Jun 2011; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5.ebuild,

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index 9e0e96b..67e1428 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -2,11 +2,11 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="4"
+EAPI=4
 
-inherit toolchain-funcs eutils
+inherit toolchain-funcs eutils fortran-2
 
-DESCRIPTION="A suite of programs for carrying out complete molecular mechanics investigations"
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
 HOMEPAGE="http://ambermd.org/#AmberTools"
 SRC_URI="AmberTools-${PV}.tar.bz2"
 
@@ -14,6 +14,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="mpi openmp X"
+
 RESTRICT="fetch"
 
 RDEPEND="
@@ -36,21 +37,18 @@ pkg_nofetch() {
 }
 
 pkg_setup() {
-	if use openmp &&
-	[[ $(tc-getCC)$ == *gcc* ]] &&
-		( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
-		! has_version sys-devel/gcc[openmp] )
-	then
-		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
-		ewarn "If you want to build ${PN} with OpenMP, abort now,"
-		ewarn "and switch CC to an OpenMP capable compiler"
+	fortran-2_pkg_setup
+	if use openmp; then
+		tc-has-openmp || \
+			die "Please select an openmp capable compiler like gcc[openmp]"
 	fi
 	AMBERHOME="${S}"
 }
 
 src_prepare() {
-	epatch "${FILESDIR}/${P}-bugfix_1-18.patch"
-	epatch "${FILESDIR}/${P}-gentoo.patch"
+	epatch \
+		"${FILESDIR}/${P}-bugfix_1-18.patch" \
+		"${FILESDIR}/${P}-gentoo.patch"
 	cd AmberTools/src
 	rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die
 }

diff --git a/sci-chemistry/ambertools/ambertools-1.5.ebuild b/sci-chemistry/ambertools/ambertools-1.5.ebuild
index 776a56f..347c64b 100644
--- a/sci-chemistry/ambertools/ambertools-1.5.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.5.ebuild
@@ -2,11 +2,11 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="4"
+EAPI=4
 
-inherit toolchain-funcs eutils
+inherit toolchain-funcs eutils fortran-2
 
-DESCRIPTION="A suite of programs for carrying out complete molecular mechanics investigations"
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
 HOMEPAGE="http://ambermd.org/#AmberTools"
 SRC_URI="AmberTools-${PV}.tar.bz2"
 
@@ -14,6 +14,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="mpi openmp X"
+
 RESTRICT="fetch"
 
 RDEPEND="
@@ -38,21 +39,18 @@ pkg_nofetch() {
 }
 
 pkg_setup() {
-	if use openmp &&
-	[[ $(tc-getCC)$ == *gcc* ]] &&
-		( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
-		! has_version sys-devel/gcc[openmp] )
-	then
-		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
-		ewarn "If you want to build ${PN} with OpenMP, abort now,"
-		ewarn "and switch CC to an OpenMP capable compiler"
+	fortran-2_pkg_setup
+	if use openmp; then
+		tc-has-openmp || \
+			die "Please select an openmp capable compiler like gcc[openmp]"
 	fi
 	AMBERHOME="${S}"
 }
 
 src_prepare() {
-	epatch "${FILESDIR}/${P}-bugfix_1-3.patch"
-	epatch "${FILESDIR}/${P}-gentoo.patch"
+	epatch \
+		"${FILESDIR}/${P}-bugfix_1-3.patch" \
+		"${FILESDIR}/${P}-gentoo.patch"
 	cd AmberTools/src
 	rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die
 }



^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-06-23  9:31 Justin Lecher
  0 siblings, 0 replies; 19+ messages in thread
From: Justin Lecher @ 2011-06-23  9:31 UTC (permalink / raw
  To: gentoo-commits

commit:     fb183d44b7509695955d902e955fc66aae427460
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 23 09:27:01 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 23 09:27:01 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fb183d44

Streamlined fortran-2 eclass usage

(Portage version: 2.2.0_alpha41/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/ambertools/ChangeLog             |    4 ++++
 sci-chemistry/ambertools/ambertools-1.4.ebuild |    5 +++--
 sci-chemistry/ambertools/ambertools-1.5.ebuild |    5 +++--
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index ea945fd..9d1fcad 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  23 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild,
+  ambertools-1.5.ebuild:
+  Streamlined fortran-2 eclass usage
+
   21 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild,
   ambertools-1.5.ebuild:
   Added fortran-2.eclass support

diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index 67e1428..8820dc6 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=4
 
-inherit toolchain-funcs eutils fortran-2
+inherit eutils fortran-2 toolchain-funcs
 
 DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
 HOMEPAGE="http://ambermd.org/#AmberTools"
@@ -24,7 +24,8 @@ RDEPEND="
 	sci-libs/cifparse-obj
 	sci-chemistry/mopac7
 	sci-libs/netcdf
-	sci-chemistry/reduce"
+	sci-chemistry/reduce
+	virtual/fortran"
 DEPEND="${RDEPEND}
 	dev-util/byacc
 	dev-libs/libf2c

diff --git a/sci-chemistry/ambertools/ambertools-1.5.ebuild b/sci-chemistry/ambertools/ambertools-1.5.ebuild
index 347c64b..0788a8d 100644
--- a/sci-chemistry/ambertools/ambertools-1.5.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.5.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=4
 
-inherit toolchain-funcs eutils fortran-2
+inherit eutils fortran-2 toolchain-funcs
 
 DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
 HOMEPAGE="http://ambermd.org/#AmberTools"
@@ -26,7 +26,8 @@ RDEPEND="
 	sci-chemistry/mopac7
 	sci-libs/netcdf
 	sci-libs/fftw:2.1
-	sci-chemistry/reduce"
+	sci-chemistry/reduce
+	virtual/fortran"
 DEPEND="${RDEPEND}
 	dev-util/byacc
 	dev-libs/libf2c



^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-07-28 12:03 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-07-28 12:03 UTC (permalink / raw
  To: gentoo-commits

commit:     af2d23a6e79abd8092230d1045f9f689a776589b
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 28 12:02:48 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Jul 28 12:02:48 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=af2d23a6

[sci-chemistry/ambertools] Updates for ambertools and gcc-4.6

(Portage version: 2.2.0_alpha47/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.5-r1.ebuild |  140 +++++++++++++++++++++
 1 files changed, 140 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
new file mode 100644
index 0000000..bebe615
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
@@ -0,0 +1,140 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+	AmberTools-${PV}.tar.bz2
+	mirror://gentoo/${P}-bugfix_1-10.patch.xz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="mpi openmp X"
+
+RESTRICT="fetch"
+
+RDEPEND="
+	virtual/cblas
+	virtual/lapack
+	sci-libs/clapack
+	sci-libs/arpack
+	sci-libs/cifparse-obj
+	sci-chemistry/mopac7
+	sci-libs/netcdf
+	sci-libs/fftw:2.1
+	sci-chemistry/reduce
+	virtual/fortran"
+DEPEND="${RDEPEND}
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp"
+S="${WORKDIR}/amber11"
+
+pkg_nofetch() {
+	einfo "Go to ${HOMEPAGE} and get ${A}"
+	einfo "Place it in ${DISTDIR}"
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	if use openmp; then
+		tc-has-openmp || \
+			die "Please select an openmp capable compiler like gcc[openmp]"
+	fi
+	AMBERHOME="${S}"
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}/${P}-bugfix_1-3.patch" \
+		"${FILESDIR}/${P}-gentoo.patch"
+	cd AmberTools/src
+	rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die
+}
+
+src_configure() {
+	cd AmberTools/src
+	sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+		-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+		-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+		-e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
+		-e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
+		-e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \
+		-e "s:fc=g77:fc=$(tc-getFC):g" \
+		-e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \
+		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+		-e "s:-O3::g" \
+		-i configure || die
+	sed -e "s:arsecond_:arscnd_:g" \
+		-i sff/time.c \
+		-i sff/sff.h \
+		-i sff/sff.c || die
+	sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \
+		-i nss/Makefile || die
+
+	local myconf
+
+	use X || myconf="${myconf} -noX11"
+
+	for x in mpi openmp; do
+		use ${x} && myconf="${myconf} -${x}"
+	done
+
+	./configure \
+		${myconf} \
+		-nobintraj \
+		-nomdgx \
+		-nopython \
+		-nomtkpp \
+		gnu
+#	$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+}
+
+src_compile() {
+	cd AmberTools/src
+	emake || die
+}
+
+src_install() {
+	rm -r bin/chemistry bin/MMPBSA_mods
+	rm bin/ante-MMPBSA.py bin/extractFrcmod.py
+	for x in bin/*
+		do dobin ${x} || die
+	done
+	rm "${ED}/usr/bin/yacc"
+	dobin AmberTools/src/antechamber/mopac.sh
+	sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+		-i "${ED}/usr/bin/mopac.sh" || die
+	# Make symlinks untill binpath for amber will be fixed
+	dodir /usr/share/${PN}/bin
+	cd "${ED}/usr/bin"
+	for x in *
+		do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
+	done
+	cd "${S}"
+#	sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
+#		-i "${ED}/usr/bin/xleap" \
+#		-i "${ED}/usr/bin/tleap" || die
+	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
+	dolib.a lib/*
+	insinto /usr/include/${PN}
+	doins include/*
+	insinto /usr/share/${PN}
+	doins -r dat
+	cd AmberTools
+	doins -r benchmarks
+	doins -r examples
+	doins -r test
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
+	EOF
+	doenvd "${T}"/99ambertools
+}



^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2011-07-28 12:28 Alexey Shvetsov
  0 siblings, 0 replies; 19+ messages in thread
From: Alexey Shvetsov @ 2011-07-28 12:28 UTC (permalink / raw
  To: gentoo-commits

commit:     b579add2961243d89259622f8af0886ff0d76819
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 28 12:27:39 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Jul 28 12:27:39 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b579add2

[sci-chemistry/ambertools] Fix typo

(Portage version: 2.2.0_alpha47/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/ambertools/ambertools-1.5-r1.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
index bebe615..da44cf5 100644
--- a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
@@ -52,7 +52,7 @@ pkg_setup() {
 
 src_prepare() {
 	epatch \
-		"${WORKDIR}/${P}-bugfix_1-3.patch" \
+		"${WORKDIR}/${P}-bugfix_1-10.patch" \
 		"${FILESDIR}/${P}-gentoo.patch"
 	cd AmberTools/src
 	rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die



^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2012-10-27 17:32 Reinis Danne
  0 siblings, 0 replies; 19+ messages in thread
From: Reinis Danne @ 2012-10-27 17:32 UTC (permalink / raw
  To: gentoo-commits

commit:     4379517864dfbf89bbf5281fd9ae63811eabadd0
Author:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Sat Oct 27 17:30:13 2012 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Sat Oct 27 17:30:13 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=43795178

ambertools: export AMBERHOME in ebuild

---
 sci-chemistry/ambertools/ambertools-12.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild
index 5b5a3db..0a64bf0 100644
--- a/sci-chemistry/ambertools/ambertools-12.ebuild
+++ b/sci-chemistry/ambertools/ambertools-12.ebuild
@@ -47,7 +47,7 @@ pkg_setup() {
 		tc-has-openmp || \
 			die "Please select an openmp capable compiler like gcc[openmp]"
 	fi
-	AMBERHOME="${S}"
+	export AMBERHOME="${S}"
 }
 
 src_prepare() {


^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2012-11-08  9:39 Justin Lecher
  0 siblings, 0 replies; 19+ messages in thread
From: Justin Lecher @ 2012-11-08  9:39 UTC (permalink / raw
  To: gentoo-commits

commit:     be906dc4f12734d826960858b788e9a10358d320
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov  8 09:38:19 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Nov  8 09:38:19 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=be906dc4

sci-chemistry/ambertools: Add another fix for blas/lapack

Package-Manager: portage-2.2.0_alpha142
RepoMan-Options: --force

---
 sci-chemistry/ambertools/ChangeLog            |    8 ++++++++
 sci-chemistry/ambertools/ambertools-12.ebuild |    5 ++++-
 sci-chemistry/ambertools/metadata.xml         |    1 -
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index fb9077d..9799e43 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
+  08 Nov 2012; Justin Lecher <jlec@gentoo.org> ambertools-12.ebuild,
+  metadata.xml:
+  Add another fix for blas/lapack
+
+  08 Nov 2012; Justin Lecher <jlec@gentoo.org> ambertools-12.ebuild,
+  metadata.xml:
+  Add another fix for blas/lapack
+
   21 Oct 2012; Reinis Danne <rei4dan@gmail.com> ambertools-12.ebuild,
   files/ambertools-12-gentoo.patch:
   Fix parallel tests.

diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild
index 0a64bf0..ea7dfdb 100644
--- a/sci-chemistry/ambertools/ambertools-12.ebuild
+++ b/sci-chemistry/ambertools/ambertools-12.ebuild
@@ -71,9 +71,12 @@ src_prepare() {
 
 src_configure() {
 	cd "${S}"/AmberTools/src
-	sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+	sed \
+		-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
 		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
+		-e "s:-llapack:$(pkg-config lapack --libs) -lclapack:g" \
 		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+		-e "s:-lblas:$(pkg-config blas cblas --libs):g" \
 		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
 		-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
 		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \

diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml
index 20e218e..b2558d8 100644
--- a/sci-chemistry/ambertools/metadata.xml
+++ b/sci-chemistry/ambertools/metadata.xml
@@ -7,4 +7,3 @@
 		<name>Alexey Shvetsov</name>
 	</maintainer>
 </pkgmetadata>
-


^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2013-02-22 10:15 Justin Lecher
  0 siblings, 0 replies; 19+ messages in thread
From: Justin Lecher @ 2013-02-22 10:15 UTC (permalink / raw
  To: gentoo-commits

commit:     a46118186e3f3adf51cb1ae454fe64b5123ae4a4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 22 10:13:21 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 22 10:13:21 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a4611818

sci-chemistry/ambertools: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config

Package-Manager: portage-2.2.0_alpha163
RepoMan-Options: --force

---
 sci-chemistry/ambertools/ChangeLog                |    7 ++++++-
 sci-chemistry/ambertools/ambertools-1.5-r2.ebuild |    8 ++++----
 sci-chemistry/ambertools/ambertools-1.5-r3.ebuild |    8 ++++----
 sci-chemistry/ambertools/ambertools-1.5-r4.ebuild |    8 ++++----
 sci-chemistry/ambertools/ambertools-12.ebuild     |   14 +++++++-------
 sci-chemistry/ambertools/metadata.xml             |   10 +++++-----
 6 files changed, 30 insertions(+), 25 deletions(-)

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index 9799e43..ebc92f2 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -1,7 +1,12 @@
 # ChangeLog for sci-chemistry/ambertools
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
+  22 Feb 2013; Justin Lecher <jlec@gentoo.org> ambertools-1.5-r2.ebuild,
+  ambertools-1.5-r3.ebuild, ambertools-1.5-r4.ebuild, ambertools-12.ebuild,
+  metadata.xml:
+  Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
+
   08 Nov 2012; Justin Lecher <jlec@gentoo.org> ambertools-12.ebuild,
   metadata.xml:
   Add another fix for blas/lapack

diff --git a/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild
index 39413fd..a042b34 100644
--- a/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
@@ -73,8 +73,8 @@ src_prepare() {
 src_configure() {
 	cd "${S}"/AmberTools/src
 	sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
-		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
 		-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
 		-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
 		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
@@ -82,7 +82,7 @@ src_configure() {
 		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
 		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
 		-e "s:fc=g77:fc=$(tc-getFC):g" \
-		-e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \
+		-e "s:\$netcdflib:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
 		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
 		-i configure || die
 	sed -e "s:arsecond_:arscnd_:g" \

diff --git a/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild
index 44bd059..c1aff5e 100644
--- a/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
@@ -75,8 +75,8 @@ src_prepare() {
 src_configure() {
 	cd "${S}"/AmberTools/src
 	sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
-		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
 		-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
 		-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
 		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
@@ -84,7 +84,7 @@ src_configure() {
 		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
 		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
 		-e "s:fc=g77:fc=$(tc-getFC):g" \
-		-e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \
+		-e "s:\$netcdflib:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
 		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
 		-i configure || die
 	sed -e "s:arsecond_:arscnd_:g" \

diff --git a/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
index d689579..4765d2a 100644
--- a/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
@@ -76,8 +76,8 @@ src_prepare() {
 src_configure() {
 	cd "${S}"/AmberTools/src
 	sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
-		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
 		-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
 		-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
 		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
@@ -85,7 +85,7 @@ src_configure() {
 		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
 		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
 		-e "s:fc=g77:fc=$(tc-getFC):g" \
-		-e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \
+		-e "s:\$netcdflib:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
 		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
 		-i configure || die
 	sed -e "s:arsecond_:arscnd_:g" \

diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild
index ea7dfdb..8b7fcbb 100644
--- a/sci-chemistry/ambertools/ambertools-12.ebuild
+++ b/sci-chemistry/ambertools/ambertools-12.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -73,18 +73,18 @@ src_configure() {
 	cd "${S}"/AmberTools/src
 	sed \
 		-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
-		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
-		-e "s:-llapack:$(pkg-config lapack --libs) -lclapack:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
-		-e "s:-lblas:$(pkg-config blas cblas --libs):g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+		-e "s:-llapack:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
+		-e "s:-lblas:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
 		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
 		-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
 		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
 		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
 		-e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
-		-e "s:GENTOO_FFTW3_LIBS:$(pkg-config fftw3 --libs):" \
+		-e "s:GENTOO_FFTW3_LIBS:$($(tc-getPKG_CONFIG) fftw3 --libs):" \
 		-e "s:fc=g77:fc=$(tc-getFC):g" \
-		-e "s:\$netcdfflag:$(pkg-config netcdf --libs):g" \
+		-e "s:\$netcdfflag:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
 		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
 		-i configure2 || die
 	sed -e "s:arsecond_:arscnd_:g" \

diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml
index b2558d8..13ef0bf 100644
--- a/sci-chemistry/ambertools/metadata.xml
+++ b/sci-chemistry/ambertools/metadata.xml
@@ -1,9 +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>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>alexxy@gentoo.org</email>
+    <name>Alexey Shvetsov</name>
+  </maintainer>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2013-03-03 17:52 Justin Lecher
  0 siblings, 0 replies; 19+ messages in thread
From: Justin Lecher @ 2013-03-03 17:52 UTC (permalink / raw
  To: gentoo-commits

commit:     af7ac5ef99aa48ebd7e289f8eb3d36597c4c077e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  3 17:47:06 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  3 17:47:06 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=af7ac5ef

sci-chemistry/ambertools: Add missing multilib.eclass

Package-Manager: portage-2.2.0_alpha164
RepoMan-Options: --force

---
 sci-chemistry/ambertools/ChangeLog                |    3 +++
 sci-chemistry/ambertools/ambertools-1.5-r4.ebuild |    2 +-
 2 files changed, 4 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index d7e45a4..f4d3a9d 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
+  03 Mar 2013; Justin Lecher <jlec@gentoo.org> ambertools-1.5-r4.ebuild:
+  Add missing multilib.eclass
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> -ambertools-1.5-r2.ebuild,
   -ambertools-1.5-r3.ebuild, ambertools-12.ebuild:
   Add missing multilib.eclass

diff --git a/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
index 4765d2a..2ac4b2f 100644
--- a/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=4
 
-inherit eutils fortran-2 toolchain-funcs
+inherit eutils fortran-2 multilib toolchain-funcs
 
 DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
 HOMEPAGE="http://ambermd.org/#AmberTools"


^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2013-06-28 16:11 Christoph Junghans
  0 siblings, 0 replies; 19+ messages in thread
From: Christoph Junghans @ 2013-06-28 16:11 UTC (permalink / raw
  To: gentoo-commits

commit:     0994964c80c8cfc95089e054806257946f72c5a7
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 28 16:07:01 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jun 28 16:11:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0994964c

fixed deps

Package-Manager: portage-2.2.0_alpha185
RepoMan-Options: --force

---
 sci-chemistry/ambertools/ChangeLog            | 4 +++-
 sci-chemistry/ambertools/ambertools-12.ebuild | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index f4d3a9d..c46b0af 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
+  28 Jun 2013; Christoph Junghans <ottxor@gentoo.org> ambertools-12.ebuild:
+  fixed deps
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> ambertools-1.5-r4.ebuild:
   Add missing multilib.eclass
 
@@ -69,4 +72,3 @@
   28 Jul 2011; Alexey Shvetsov <alexxy@gentoo.org> +ambertools-1.5-r1.ebuild,
   +files/ambertools-1.5-gentoo.patch, +metadata.xml:
   Initial import to tree
-

diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild
index 70ea7f3..8324296 100644
--- a/sci-chemistry/ambertools/ambertools-12.ebuild
+++ b/sci-chemistry/ambertools/ambertools-12.ebuild
@@ -26,7 +26,7 @@ RDEPEND="
 	sci-libs/cifparse-obj
 	sci-chemistry/mopac7
 	sci-libs/netcdf
-	sci-libs/fftw:3.0
+	>=sci-libs/fftw-3.3:3.0
 	sci-chemistry/reduce"
 DEPEND="${RDEPEND}
 	app-shells/tcsh


^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/
@ 2016-01-22  8:15 Justin Lecher
  0 siblings, 0 replies; 19+ messages in thread
From: Justin Lecher @ 2016-01-22  8:15 UTC (permalink / raw
  To: gentoo-commits

commit:     1219b4dd29cdb183677c9e15a8d766a383f80770
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 22 08:15:50 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jan 22 08:15:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1219b4dd

sci-chemistry/ambertools: Fix symlinken in bin dir

Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .../{ambertools-12_p38.ebuild => ambertools-12_p38-r1.ebuild}       | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/ambertools/ambertools-12_p38.ebuild b/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild
similarity index 97%
rename from sci-chemistry/ambertools/ambertools-12_p38.ebuild
rename to sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild
index 1c907c4..e6beea2 100644
--- a/sci-chemistry/ambertools/ambertools-12_p38.ebuild
+++ b/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -144,8 +144,8 @@ src_install() {
 	# Make symlinks untill binpath for amber will be fixed
 	dodir /usr/share/${PN}/bin
 	cd "${ED}/usr/bin" || die
-	for x in *
-		do dosym /usr/bin/${x} ../share/${PN}/bin/${x}
+	for x in *; do
+		dosym ../../../bin/${x} /usr/share/${PN}/bin/${x}
 	done
 	cd "${S}" || die
 


^ permalink raw reply related	[flat|nested] 19+ messages in thread

end of thread, other threads:[~2016-01-22  8:16 UTC | newest]

Thread overview: 19+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2011-07-28 12:28 [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/ Alexey Shvetsov
  -- strict thread matches above, loose matches on Subject: below --
2016-01-22  8:15 Justin Lecher
2013-06-28 16:11 Christoph Junghans
2013-03-03 17:52 Justin Lecher
2013-02-22 10:15 Justin Lecher
2012-11-08  9:39 Justin Lecher
2012-10-27 17:32 Reinis Danne
2011-07-28 12:03 Alexey Shvetsov
2011-06-23  9:31 Justin Lecher
2011-06-21 11:54 Justin Lecher
2011-03-15 10:23 Justin Lecher
2011-03-07 18:34 Alexey Shvetsov
2011-03-07 18:28 Alexey Shvetsov
2011-03-07 18:23 Alexey Shvetsov
2011-03-07 18:20 Alexey Shvetsov
2011-03-07 18:20 Alexey Shvetsov
2011-03-07  1:55 Alexey Shvetsov
2011-03-07  1:49 Alexey Shvetsov
2011-03-07  1:49 Alexey Shvetsov

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