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* [gentoo-commits] proj/sci:master commit in: sci-chemistry/mdsctk/
@ 2013-06-02 17:40 Christoph Junghans
  0 siblings, 0 replies; 8+ messages in thread
From: Christoph Junghans @ 2013-06-02 17:40 UTC (permalink / raw
  To: gentoo-commits

commit:     bc4bf551f3e119a3960e469530cc3695bd80cc92
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Jun  2 17:40:15 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Jun  2 17:40:26 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bc4bf551

initial commit

Package-Manager: portage-2.2.0_alpha177

---
 sci-chemistry/mdsctk/ChangeLog           |  9 ++++++
 sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild | 51 ++++++++++++++++++++++++++++++++
 sci-chemistry/mdsctk/metadata.xml        | 12 ++++++++
 3 files changed, 72 insertions(+)

diff --git a/sci-chemistry/mdsctk/ChangeLog b/sci-chemistry/mdsctk/ChangeLog
new file mode 100644
index 0000000..83aa8bc
--- /dev/null
+++ b/sci-chemistry/mdsctk/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-chemistry/mdsctk
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mdsctk-1.0.0 (02 Jun 2013)
+
+  02 Jun 2013; Christoph Junghans <ottxor@gentoo.org> +mdsctk-1.0.0.ebuild,
+  +metadata.xml:
+  initial commit

diff --git a/sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild b/sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild
new file mode 100644
index 0000000..5601f7e
--- /dev/null
+++ b/sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit db-use toolchain-funcs
+
+DESCRIPTION="Molecular Dynamics Spectral Clustering Toolkit"
+HOMEPAGE="http://cnls.lanl.gov/~jphillips/?page_id=45"
+SRC_URI="http://cnls.lanl.gov/~jphillips/wp-content/uploads/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="examples R"
+
+DEPEND="
+	sci-chemistry/gromacs
+	sci-libs/gsl
+	sys-libs/db[cxx]
+	virtual/blas
+	virtual/lapack
+	R? ( dev-lang/R )
+	"
+RDEPEND="${DEPEND}"
+
+src_compile() {
+	local libdb=$(db_libname)
+	emake CPP=$(tc-getCXX) \
+		CFLAGS="${CXXFLAGS} $($(tc-getPKG_CONFIG) --cflags libgmx) \
+			$($(tc-getPKG_CONFIG) --cflags gsl) \
+			$($(tc-getPKG_CONFIG) --cflags lapack) \
+			$($(tc-getPKG_CONFIG) --cflags blas) \
+			-I$(db_includedir)" \
+		LIBS="$($(tc-getPKG_CONFIG) --libs libgmx) -lgmxana \
+			$($(tc-getPKG_CONFIG) --libs gsl) \
+			$($(tc-getPKG_CONFIG) --libs lapack) \
+			$($(tc-getPKG_CONFIG) --libs blas) \
+			-l${libdb/db/db_cxx} ${LDFLAGS}" \
+		OPTIONS=""
+}
+
+src_install() {
+	dodoc AUTHORS README
+	dobin auto_decomp_sparse bb_xtc_to_phipsi check_xtc decomp_sparse knn_data \
+		knn_rms knn_rms_sparse make_sparse phipsi_to_sincos rms_test
+	use R && dobin clustering_histogram.r  clustering_nmi.r  kmeans.r plot_histogram.r
+	insinto /usr/share/"${PN}"/examples
+	use examples && doins -r examples
+}

diff --git a/sci-chemistry/mdsctk/metadata.xml b/sci-chemistry/mdsctk/metadata.xml
new file mode 100644
index 0000000..d24286a
--- /dev/null
+++ b/sci-chemistry/mdsctk/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>ottxor@gentoo.org</email>
+		<name>Christoph Junghans</name>
+	</maintainer>
+	<use>
+		<flag name="R">Install <pkg>dev-lang/R</pkg> as well</flag>
+	</use>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/mdsctk/
@ 2013-06-03 23:31 Christoph Junghans
  0 siblings, 0 replies; 8+ messages in thread
From: Christoph Junghans @ 2013-06-03 23:31 UTC (permalink / raw
  To: gentoo-commits

commit:     c20fe59cecebe309fe24a563e9a0bfd9356e2216
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jun  3 23:30:51 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jun  3 23:31:13 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c20fe59c

added ~amd64-linux + clean up

Package-Manager: portage-2.2.0_alpha177

---
 sci-chemistry/mdsctk/ChangeLog           | 4 ++++
 sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild | 4 ++--
 sci-chemistry/mdsctk/metadata.xml        | 2 +-
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/mdsctk/ChangeLog b/sci-chemistry/mdsctk/ChangeLog
index 83aa8bc..ca0cede 100644
--- a/sci-chemistry/mdsctk/ChangeLog
+++ b/sci-chemistry/mdsctk/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Jun 2013; Christoph Junghans <ottxor@gentoo.org> mdsctk-1.0.0.ebuild,
+  metadata.xml:
+  added ~amd64-linux + clean up
+
 *mdsctk-1.0.0 (02 Jun 2013)
 
   02 Jun 2013; Christoph Junghans <ottxor@gentoo.org> +mdsctk-1.0.0.ebuild,

diff --git a/sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild b/sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild
index 5601f7e..84093b0 100644
--- a/sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild
+++ b/sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild
@@ -12,11 +12,11 @@ SRC_URI="http://cnls.lanl.gov/~jphillips/wp-content/uploads/${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~amd64-linux"
 IUSE="examples R"
 
 DEPEND="
-	sci-chemistry/gromacs
+	sci-chemistry/gromacs:=
 	sci-libs/gsl
 	sys-libs/db[cxx]
 	virtual/blas

diff --git a/sci-chemistry/mdsctk/metadata.xml b/sci-chemistry/mdsctk/metadata.xml
index d24286a..3909537 100644
--- a/sci-chemistry/mdsctk/metadata.xml
+++ b/sci-chemistry/mdsctk/metadata.xml
@@ -7,6 +7,6 @@
 		<name>Christoph Junghans</name>
 	</maintainer>
 	<use>
-		<flag name="R">Install <pkg>dev-lang/R</pkg> as well</flag>
+		<flag name="R">Install <pkg>dev-lang/R</pkg> scripts as well</flag>
 	</use>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/mdsctk/
@ 2013-07-04 19:10 Christoph Junghans
  0 siblings, 0 replies; 8+ messages in thread
From: Christoph Junghans @ 2013-07-04 19:10 UTC (permalink / raw
  To: gentoo-commits

commit:     8493aae69cb0cf38bd8ec300f0783d83b8991b5e
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jul  4 19:09:42 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jul  4 19:09:42 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8493aae6

version bump

Package-Manager: portage-2.2.0_alpha186

---
 sci-chemistry/mdsctk/ChangeLog                     |  6 +++++
 .../{mdsctk-1.0.0.ebuild => mdsctk-1.1.0.ebuild}   | 29 +++++++++-------------
 2 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/sci-chemistry/mdsctk/ChangeLog b/sci-chemistry/mdsctk/ChangeLog
index ca0cede..1059cbb 100644
--- a/sci-chemistry/mdsctk/ChangeLog
+++ b/sci-chemistry/mdsctk/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*mdsctk-1.1.0 (04 Jul 2013)
+
+  04 Jul 2013; Christoph Junghans <ottxor@gentoo.org> +mdsctk-1.1.0.ebuild,
+  -mdsctk-1.0.0.ebuild:
+  version bump
+
   03 Jun 2013; Christoph Junghans <ottxor@gentoo.org> mdsctk-1.0.0.ebuild,
   metadata.xml:
   added ~amd64-linux + clean up

diff --git a/sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild b/sci-chemistry/mdsctk/mdsctk-1.1.0.ebuild
similarity index 51%
rename from sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild
rename to sci-chemistry/mdsctk/mdsctk-1.1.0.ebuild
index 84093b0..2f7ac10 100644
--- a/sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild
+++ b/sci-chemistry/mdsctk/mdsctk-1.1.0.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-inherit db-use toolchain-funcs
+inherit cmake-utils db-use toolchain-funcs
 
 DESCRIPTION="Molecular Dynamics Spectral Clustering Toolkit"
 HOMEPAGE="http://cnls.lanl.gov/~jphillips/?page_id=45"
@@ -21,31 +21,26 @@ DEPEND="
 	sys-libs/db[cxx]
 	virtual/blas
 	virtual/lapack
+	sci-libs/arpack
 	R? ( dev-lang/R )
 	"
 RDEPEND="${DEPEND}"
 
-src_compile() {
-	local libdb=$(db_libname)
-	emake CPP=$(tc-getCXX) \
-		CFLAGS="${CXXFLAGS} $($(tc-getPKG_CONFIG) --cflags libgmx) \
-			$($(tc-getPKG_CONFIG) --cflags gsl) \
-			$($(tc-getPKG_CONFIG) --cflags lapack) \
-			$($(tc-getPKG_CONFIG) --cflags blas) \
-			-I$(db_includedir)" \
-		LIBS="$($(tc-getPKG_CONFIG) --libs libgmx) -lgmxana \
-			$($(tc-getPKG_CONFIG) --libs gsl) \
-			$($(tc-getPKG_CONFIG) --libs lapack) \
-			$($(tc-getPKG_CONFIG) --libs blas) \
-			-l${libdb/db/db_cxx} ${LDFLAGS}" \
-		OPTIONS=""
+src_configure() {
+	# all this hacking is due to the fact that check_include_file_cxx
+	# has no support for CMAKE_{SYSTEM_,}_INCLUDE_PATH, so we fake it
+	# using CMAKE_REQUIRED_INCLUDES and a symlink
+	local mycmakeargs=( -DCMAKE_REQUIRED_INCLUDES="$(db_includedir)" )
+	cmake-utils_src_configure
+	ln -s "$(db_includedir)"/db_cxx.h "${BUILD_DIR}" || die
 }
 
 src_install() {
 	dodoc AUTHORS README
-	dobin auto_decomp_sparse bb_xtc_to_phipsi check_xtc decomp_sparse knn_data \
-		knn_rms knn_rms_sparse make_sparse phipsi_to_sincos rms_test
 	use R && dobin clustering_histogram.r  clustering_nmi.r  kmeans.r plot_histogram.r
 	insinto /usr/share/"${PN}"/examples
 	use examples && doins -r examples
+	cd "${BUILD_DIR}" || die
+	dobin auto_decomp_sparse auto_decomp_sparse_nystrom bb_xtc_to_phipsi check_xtc decomp_sparse decomp_sparse_nystrom \
+		knn_data knn_rms make_sysparse make_gesparse phipsi_to_sincos rms_test split_xtc
 }


^ permalink raw reply related	[flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/mdsctk/
@ 2013-12-12 16:12 Christoph Junghans
  0 siblings, 0 replies; 8+ messages in thread
From: Christoph Junghans @ 2013-12-12 16:12 UTC (permalink / raw
  To: gentoo-commits

commit:     bd2996a3ef34e41240b30796e7576de0b744c39d
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 12 16:11:48 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Dec 12 16:11:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bd2996a3

version bump

Package-Manager: portage-2.2.7

---
 sci-chemistry/mdsctk/ChangeLog                            |  6 ++++++
 .../mdsctk/{mdsctk-1.1.0.ebuild => mdsctk-1.2.0.ebuild}   | 15 ++++++---------
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/sci-chemistry/mdsctk/ChangeLog b/sci-chemistry/mdsctk/ChangeLog
index 1059cbb..91fb1c7 100644
--- a/sci-chemistry/mdsctk/ChangeLog
+++ b/sci-chemistry/mdsctk/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*mdsctk-1.2.0 (12 Dec 2013)
+
+  12 Dec 2013; Christoph Junghans <ottxor@gentoo.org> +mdsctk-1.2.0.ebuild,
+  -mdsctk-1.1.0.ebuild:
+  version bump
+
 *mdsctk-1.1.0 (04 Jul 2013)
 
   04 Jul 2013; Christoph Junghans <ottxor@gentoo.org> +mdsctk-1.1.0.ebuild,

diff --git a/sci-chemistry/mdsctk/mdsctk-1.1.0.ebuild b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
similarity index 64%
rename from sci-chemistry/mdsctk/mdsctk-1.1.0.ebuild
rename to sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
index 2f7ac10..80629e8 100644
--- a/sci-chemistry/mdsctk/mdsctk-1.1.0.ebuild
+++ b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
@@ -7,8 +7,8 @@ EAPI=5
 inherit cmake-utils db-use toolchain-funcs
 
 DESCRIPTION="Molecular Dynamics Spectral Clustering Toolkit"
-HOMEPAGE="http://cnls.lanl.gov/~jphillips/?page_id=45"
-SRC_URI="http://cnls.lanl.gov/~jphillips/wp-content/uploads/${P}.tar.gz"
+HOMEPAGE="https://github.com/douradopalmares/mdsctk"
+SRC_URI="https://github.com/douradopalmares/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~amd64-linux"
 IUSE="examples R"
 
 DEPEND="
-	sci-chemistry/gromacs:=
+	=sci-chemistry/gromacs-4.6*:=
 	sci-libs/gsl
 	sys-libs/db[cxx]
 	virtual/blas
@@ -27,16 +27,13 @@ DEPEND="
 RDEPEND="${DEPEND}"
 
 src_configure() {
-	# all this hacking is due to the fact that check_include_file_cxx
-	# has no support for CMAKE_{SYSTEM_,}_INCLUDE_PATH, so we fake it
-	# using CMAKE_REQUIRED_INCLUDES and a symlink
-	local mycmakeargs=( -DCMAKE_REQUIRED_INCLUDES="$(db_includedir)" )
+	echo 'include_directories(${DB_CXX_INCLUDE_PATH})' >> CMakeLists.txt
+	local mycmakeargs=( -DDB_CXX_INCLUDE_PATH="$(db_includedir)" )
 	cmake-utils_src_configure
-	ln -s "$(db_includedir)"/db_cxx.h "${BUILD_DIR}" || die
 }
 
 src_install() {
-	dodoc AUTHORS README
+	dodoc AUTHORS README.md
 	use R && dobin clustering_histogram.r  clustering_nmi.r  kmeans.r plot_histogram.r
 	insinto /usr/share/"${PN}"/examples
 	use examples && doins -r examples


^ permalink raw reply related	[flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/mdsctk/
@ 2013-12-14 22:29 Christoph Junghans
  0 siblings, 0 replies; 8+ messages in thread
From: Christoph Junghans @ 2013-12-14 22:29 UTC (permalink / raw
  To: gentoo-commits

commit:     ba29197735efad502c4fb79e1d271903012dd152
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 14 22:29:41 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Dec 14 22:29:41 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ba291977

fixed install

Package-Manager: portage-2.2.7

---
 sci-chemistry/mdsctk/ChangeLog           | 3 +++
 sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild | 3 ++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/mdsctk/ChangeLog b/sci-chemistry/mdsctk/ChangeLog
index 91fb1c7..7fd81d3 100644
--- a/sci-chemistry/mdsctk/ChangeLog
+++ b/sci-chemistry/mdsctk/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  14 Dec 2013; Christoph Junghans <ottxor@gentoo.org> mdsctk-1.2.0.ebuild:
+  fixed install
+
 *mdsctk-1.2.0 (12 Dec 2013)
 
   12 Dec 2013; Christoph Junghans <ottxor@gentoo.org> +mdsctk-1.2.0.ebuild,

diff --git a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
index 80629e8..63a45e2 100644
--- a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
+++ b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
@@ -34,7 +34,8 @@ src_configure() {
 
 src_install() {
 	dodoc AUTHORS README.md
-	use R && dobin clustering_histogram.r  clustering_nmi.r  kmeans.r plot_histogram.r
+	use R && dobin clustering_nmi.r  clustering_pdf.r  density.r  entropy.r  kmeans.r  mdsctk.r  plot_pdf.r \
+		probability.r
 	insinto /usr/share/"${PN}"/examples
 	use examples && doins -r examples
 	cd "${BUILD_DIR}" || die


^ permalink raw reply related	[flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/mdsctk/
@ 2015-03-08 18:08 Justin Lecher
  0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2015-03-08 18:08 UTC (permalink / raw
  To: gentoo-commits

commit:     0dc80980e6ce9efbe9c9d8610c9ce2be11d80819
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  8 18:08:47 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  8 18:08:47 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0dc80980

fix SLOT operator; drop KEYWORDS as deps are missing

Package-Manager: portage-2.2.17
RepoMan-Options: --force

 sci-chemistry/mdsctk/ChangeLog           |  6 +++++-
 sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild |  6 +++---
 sci-chemistry/mdsctk/metadata.xml        | 16 ++++++++--------
 3 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/sci-chemistry/mdsctk/ChangeLog b/sci-chemistry/mdsctk/ChangeLog
index 7fd81d3..d90a33d 100644
--- a/sci-chemistry/mdsctk/ChangeLog
+++ b/sci-chemistry/mdsctk/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-chemistry/mdsctk
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  08 Mar 2015; Justin Lecher <jlec@gentoo.org> mdsctk-1.2.0.ebuild,
+  metadata.xml:
+  fix SLOT operator; drop KEYWORDS as deps are missing
+
   14 Dec 2013; Christoph Junghans <ottxor@gentoo.org> mdsctk-1.2.0.ebuild:
   fixed install
 

diff --git a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
index 8af615e..5bb8046 100644
--- a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
+++ b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -12,13 +12,13 @@ SRC_URI="https://github.com/douradopalmares/${PN}/archive/${PV}.tar.gz -> ${P}.t
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64 ~amd64-linux"
+KEYWORDS=""
 IUSE="examples R"
 
 DEPEND="
 	=sci-chemistry/gromacs-4.6*:=
 	sci-libs/gsl
-	sys-libs/db[cxx]
+	sys-libs/db:=[cxx]
 	virtual/blas
 	virtual/lapack
 	sci-libs/arpack

diff --git a/sci-chemistry/mdsctk/metadata.xml b/sci-chemistry/mdsctk/metadata.xml
index 3909537..a60809e 100644
--- a/sci-chemistry/mdsctk/metadata.xml
+++ b/sci-chemistry/mdsctk/metadata.xml
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>ottxor@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<use>
-		<flag name="R">Install <pkg>dev-lang/R</pkg> scripts as well</flag>
-	</use>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>ottxor@gentoo.org</email>
+    <name>Christoph Junghans</name>
+  </maintainer>
+  <use>
+    <flag name="R">Install <pkg>dev-lang/R</pkg> scripts as well</flag>
+  </use>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/mdsctk/
@ 2015-06-05 11:20 Justin Lecher
  0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2015-06-05 11:20 UTC (permalink / raw
  To: gentoo-commits

commit:     7f0738f81b0f81cfa2c7c7650f391b1021135216
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun  5 11:14:30 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun  5 11:14:30 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f0738f8

sci-chemistry/mdsctk: Add github to remote-id in metadata.xml

Package-Manager: portage-2.2.20

 sci-chemistry/mdsctk/ChangeLog    | 3 +++
 sci-chemistry/mdsctk/metadata.xml | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/sci-chemistry/mdsctk/ChangeLog b/sci-chemistry/mdsctk/ChangeLog
index d90a33d..a3307e9 100644
--- a/sci-chemistry/mdsctk/ChangeLog
+++ b/sci-chemistry/mdsctk/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+  sci-chemistry/mdsctk: Add github to remote-id in metadata.xml
+
   08 Mar 2015; Justin Lecher <jlec@gentoo.org> mdsctk-1.2.0.ebuild,
   metadata.xml:
   fix SLOT operator; drop KEYWORDS as deps are missing

diff --git a/sci-chemistry/mdsctk/metadata.xml b/sci-chemistry/mdsctk/metadata.xml
index a60809e..d9fa95a 100644
--- a/sci-chemistry/mdsctk/metadata.xml
+++ b/sci-chemistry/mdsctk/metadata.xml
@@ -9,4 +9,7 @@
   <use>
     <flag name="R">Install <pkg>dev-lang/R</pkg> scripts as well</flag>
   </use>
+  <upstream>
+    <remote-id type="github">douradopalmares/mdsctk</remote-id>
+  </upstream>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/mdsctk/
@ 2021-01-05 19:21 Andrew Ammerlaan
  0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2021-01-05 19:21 UTC (permalink / raw
  To: gentoo-commits

commit:     1286cafb69a932e2f236c37867fcbbc07142a323
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan  5 19:19:27 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan  5 19:20:34 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1286cafb

sci-chemistry/mdsctk: drop pack, last update 2015, no compat w. gromacs::gentoo

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild | 43 --------------------------------
 sci-chemistry/mdsctk/metadata.xml        | 18 -------------
 2 files changed, 61 deletions(-)

diff --git a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
deleted file mode 100644
index 1a099e69c..000000000
--- a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils db-use toolchain-funcs
-
-DESCRIPTION="Molecular Dynamics Spectral Clustering Toolkit"
-HOMEPAGE="https://github.com/douradopalmares/mdsctk"
-SRC_URI="https://github.com/douradopalmares/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="examples R"
-
-DEPEND="
-	=sci-chemistry/gromacs-4.6*:=
-	sci-libs/gsl
-	sys-libs/db:=[cxx]
-	virtual/blas
-	virtual/lapack
-	sci-libs/arpack
-	R? ( dev-lang/R )
-	"
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	echo 'include_directories(${DB_CXX_INCLUDE_PATH})' >> CMakeLists.txt
-	local mycmakeargs=( -DDB_CXX_INCLUDE_PATH="$(db_includedir)" )
-	cmake-utils_src_configure
-}
-
-src_install() {
-	dodoc AUTHORS README.md
-	use R && dobin clustering_nmi.r  clustering_pdf.r  density.r  entropy.r  kmeans.r  mdsctk.r  plot_pdf.r \
-		probability.r
-	insinto /usr/share/"${PN}"/examples
-	use examples && doins -r examples
-	cd "${BUILD_DIR}" || die
-	dobin auto_decomp_sparse auto_decomp_sparse_nystrom bb_xtc_to_phipsi check_xtc decomp_sparse decomp_sparse_nystrom \
-		knn_data knn_rms make_sysparse make_gesparse phipsi_to_sincos rms_test split_xtc
-}

diff --git a/sci-chemistry/mdsctk/metadata.xml b/sci-chemistry/mdsctk/metadata.xml
deleted file mode 100644
index 466c91299..000000000
--- a/sci-chemistry/mdsctk/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>ottxor@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<use>
-		<flag name="R">Install <pkg>dev-lang/R</pkg> scripts as well</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">douradopalmares/mdsctk</remote-id>
-	</upstream>
-</pkgmetadata>


^ permalink raw reply related	[flat|nested] 8+ messages in thread
end of thread, other threads:[~2021-01-05 19:21 UTC | newest]

Thread overview: 8+ messages (download: mbox.gz follow: Atom feed
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2015-06-05 11:20 [gentoo-commits] proj/sci:master commit in: sci-chemistry/mdsctk/ Justin Lecher
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2021-01-05 19:21 Andrew Ammerlaan
2015-03-08 18:08 Justin Lecher
2013-12-14 22:29 Christoph Junghans
2013-12-12 16:12 Christoph Junghans
2013-07-04 19:10 Christoph Junghans
2013-06-03 23:31 Christoph Junghans
2013-06-02 17:40 Christoph Junghans

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