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

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

[Christoph Junghans]

commit:     38d06fad8d955c16b9ddeb8ea3160c88ac33e4de
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 19 16:55:20 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Feb 19 17:13:14 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=38d06fad

updated package.mask

---
 profiles/package.mask |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1b9c10d..7b61f75 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -80,6 +80,7 @@ sci-biology/tablet-bin
 # mask live ebuilds
 =sci-libs/votca-tools-9999
 =sci-chemistry/votca-csg-9999
+=app-doc/votca-manual-9999
 
 # Justin Lecher (jlec) (08 Jun 09)
 # jlec@gentoo.org

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

[Christoph Junghans]

commit:     1012811956ed8ab0974bc3e3671237d530253759
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 10 20:01:51 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Thu Mar 10 20:01:51 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=10128119

updated package.mask

---
 profiles/package.mask |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 7b61f75..8904894 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -80,7 +80,7 @@ sci-biology/tablet-bin
 # mask live ebuilds
 =sci-libs/votca-tools-9999
 =sci-chemistry/votca-csg-9999
-=app-doc/votca-manual-9999
+=app-doc/votca-csg-manual-9999
 
 # Justin Lecher (jlec) (08 Jun 09)
 # jlec@gentoo.org

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

[Justin Lecher]

commit:     a14bab9b4d6a054febe3fb419c482ded77cd0d83
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 17 07:52:31 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 17 07:52:31 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a14bab9b

sci-libs/vtk moved to tree and unmasked.

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/package.mask |    7 -------
 1 files changed, 0 insertions(+), 7 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 8904894..6a63b1e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -116,10 +116,3 @@ sci-biology/tablet-bin
 # mask for removal in 30d since there is no source anymore
 # (fetch restricted, and the ftp server does not respond; no hint of program at HOMEPAGE)
 sci-biology/newbler
-
-# Francois Bissey (kiwifb) (27 Oct 2010)
-# f.r.bissey@massey.ac.nz
-# mask vtk-5.6.1 as there are no stable versions in the tree
-# Avoid accidental upgrade
-=sci-libs/vtk-5.6.1
-

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

[Christoph Junghans]

commit:     ad7a4a43321d1ae4df00a5ba746af9bc6aa03050
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 20 13:15:33 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Apr 20 13:15:33 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ad7a4a43

updated package.mask

---
 profiles/package.mask |   17 +++++++++++------
 1 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 6a63b1e..a83b083 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -57,18 +57,23 @@ sci-biology/tablet-bin
 # mask live ebuild
 =sci-chemistry/burrow-owl-9999_pre15
 
-# Christoph Junghans (ottxor) (23 Jan 1<F2>)
-# kleiner_otti@gmx.de
+# Christoph Junghans (ottxor) (23 Jan 11)
+# ottxor@gentoo.org
 # mask live ebuild
 =sys-cluster/nullmpi-9999
 
+# Christoph Junghans (ottxor) (20 Apr 11)
+# ottxor@gentoo.org
+# mask live ebuild
+=sci-physics/espresso-9999
+
 # Christoph Junghans (ottxor) (03 Oct 10)
-# kleiner_otti@gmx.de
+# ottxor@gentoo.org
 # masked for testing
 =sci-libs/openmm-2.0
 
 # Christoph Junghans (ottxor) (31 Jul 10)
-# kleiner_otti@gmx.de
+# ottxor@gentoo.org
 # mask live ebuilds
 =sci-chemistry/gromacs-4.0.9999
 =sci-chemistry/gromacs-4.5.9999
@@ -76,7 +81,7 @@ sci-biology/tablet-bin
 =app-doc/gromacs-manual-9999
 
 # Christoph Junghans (ottxor) (23 Jan 10)
-# kleiner_otti@gmx.de
+# ottxor@gentoo.org
 # mask live ebuilds
 =sci-libs/votca-tools-9999
 =sci-chemistry/votca-csg-9999
@@ -90,7 +95,7 @@ sci-biology/tablet-bin
 =sci-chemistry/pymol-9999
 
 # Christoph Junghans (ottxor) (02 Nov 09)
-# kleiner_otti@gmx.de
+# ottxor@gentoo.org
 # live cvs ebuild, deps changing constantly
 # report to bug #232363
 =sci-visualization/gnuplot-4.4.9999

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

[Justin Lecher]

commit:     5a289cda4e56c501ac5f6060e028b2af9f7946bf
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 15:05:02 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 15:05:02 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5a289cda

mask sci-libs/pfft as fftw-3.3 is masked

---
 profiles/package.mask |   12 ++++++++----
 1 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index a83b083..af66aae 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher <jlec@gentoo.org> (24 Jun 2011)
+# fftw dep is masked
+sci-libs/pfft
+
 # Sebastien Fabbro (07 Jan 2011)
 # svn trunk development of root
 >=sci-physics/root-9999
@@ -52,22 +56,22 @@ sci-biology/tablet-bin
 # alpha software
 >=sci-libs/fftw-3.3_alpha1
 
-# Justin Lecher (jlec) (1 Aug 09)
+# Justin Lecher (jlec) (1 Aug 2009)
 # jlec@gentoo.org
 # mask live ebuild
 =sci-chemistry/burrow-owl-9999_pre15
 
-# Christoph Junghans (ottxor) (23 Jan 11)
+# Christoph Junghans (ottxor) (23 Jan 2011)
 # ottxor@gentoo.org
 # mask live ebuild
 =sys-cluster/nullmpi-9999
 
-# Christoph Junghans (ottxor) (20 Apr 11)
+# Christoph Junghans (ottxor) (20 Apr 2011)
 # ottxor@gentoo.org
 # mask live ebuild
 =sci-physics/espresso-9999
 
-# Christoph Junghans (ottxor) (03 Oct 10)
+# Christoph Junghans (ottxor) (03 Oct 2010)
 # ottxor@gentoo.org
 # masked for testing
 =sci-libs/openmm-2.0

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

[Justin Lecher]

commit:     87a41b033ac59e7bc921094e50df90ac39f70ccf
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 15:29:35 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 15:29:35 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=87a41b03

removed uneeded entry

---
 profiles/package.mask |    4 ----
 1 files changed, 0 insertions(+), 4 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index af66aae..4d06ddd 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,10 +34,6 @@
 # fftw dep is masked
 sci-libs/pfft
 
-# Sebastien Fabbro (07 Jan 2011)
-# svn trunk development of root
->=sci-physics/root-9999
-
 # Justin Lecher <jlec> (04 Jan 2011)
 # Masked for several QA reasons:
 # portage screams during processing this ebuild

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

[Justin Lecher]

commit:     065cfa82bb78aedc4bed5f474eadb42981cac156
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 16:17:18 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 16:17:18 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=065cfa82

Mask sci-visualization/vtkPOFFReader as paraview-3.8 is masked

---
 profiles/package.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index b637fdd..3e279a9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,6 +34,10 @@
 # fftw dep is masked
 sci-libs/pfft
 
+# Justin Lecher <jlec@gentoo.org> (24 Jun 2011)
+# paraview dep is masked
+sci-visualization/vtkPOFFReader
+
 # Justin Lecher <jlec@gentoo.org> (04 Jan 2011)
 # Masked for several QA reasons:
 # portage screams during processing this ebuild

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

[Justin Lecher]

commit:     a3000aa27b36f1cdb90a7d5c46cd3029024fb1fe
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 16:16:22 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 16:16:22 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a3000aa2

QA on package.mask

---
 profiles/package.mask |   75 ++++++++++++++++++------------------------------
 1 files changed, 28 insertions(+), 47 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 4d06ddd..b637fdd 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,7 +34,7 @@
 # fftw dep is masked
 sci-libs/pfft
 
-# Justin Lecher <jlec> (04 Jan 2011)
+# Justin Lecher <jlec@gentoo.org> (04 Jan 2011)
 # Masked for several QA reasons:
 # portage screams during processing this ebuild
 # Author uses @gentoo.org address, although not a dev
@@ -48,76 +48,57 @@ sci-libs/pfft
 # #348029
 sci-biology/tablet-bin
 
-# Sebastien Fabbro (29 Sep 2010)
-# alpha software
->=sci-libs/fftw-3.3_alpha1
-
-# Justin Lecher (jlec) (1 Aug 2009)
-# jlec@gentoo.org
+# Christoph Junghans <ottxor@gentoo.org> (20 Apr 2011)
 # mask live ebuild
-=sci-chemistry/burrow-owl-9999_pre15
+=sci-physics/espresso-9999
 
-# Christoph Junghans (ottxor) (23 Jan 2011)
-# ottxor@gentoo.org
+# Christoph Junghans <ottxor@gentoo.org> (23 Jan 2011)
 # mask live ebuild
 =sys-cluster/nullmpi-9999
 
-# Christoph Junghans (ottxor) (20 Apr 2011)
-# ottxor@gentoo.org
-# mask live ebuild
-=sci-physics/espresso-9999
+# Francois Bissey (kiwifb) (29 Oct 2010)
+# f.r.bissey@massey.ac.nz
+# mask paraview-3.8.* as there are no stable versions in the tree
+# Avoid accidental upgrade
+>=sci-visualization/paraview-3.8.0
 
-# Christoph Junghans (ottxor) (03 Oct 2010)
-# ottxor@gentoo.org
+# Christoph Junghans <ottxor@gentoo.org> (03 Oct 2010)
 # masked for testing
 =sci-libs/openmm-2.0
 
-# Christoph Junghans (ottxor) (31 Jul 10)
-# ottxor@gentoo.org
+# Sebastien Fabbro (29 Sep 2010)
+# alpha software
+>=sci-libs/fftw-3.3_alpha1
+
+# Christoph Junghans <ottxor@gentoo.org> (31 Jul 2010)
 # mask live ebuilds
 =sci-chemistry/gromacs-4.0.9999
 =sci-chemistry/gromacs-4.5.9999
 =sci-chemistry/gromacs-9999
 =app-doc/gromacs-manual-9999
 
-# Christoph Junghans (ottxor) (23 Jan 10)
-# ottxor@gentoo.org
+# Christoph Junghans <ottxor@gentoo.org> (23 Jan 2010)
 # mask live ebuilds
 =sci-libs/votca-tools-9999
 =sci-chemistry/votca-csg-9999
 =app-doc/votca-csg-manual-9999
 
-# Justin Lecher (jlec) (08 Jun 09)
-# jlec@gentoo.org
-# mask live ebuilds
-=sci-chemistry/pymol-apbs-plugin-9999
-=sci-chemistry/coot-9999
-=sci-chemistry/pymol-9999
-
-# Christoph Junghans (ottxor) (02 Nov 09)
-# ottxor@gentoo.org
+# Christoph Junghans <ottxor@gentoo.org> (02 Nov 2009)
 # live cvs ebuild, deps changing constantly
 # report to bug #232363
 =sci-visualization/gnuplot-4.4.9999
 =sci-visualization/gnuplot-4.5.9999
 
-# Justin Lecher (jlec) (11 May 09)
-# jlec@gentoo.org
-# work in progress 
-=sci-chemistry/almost-1.0.3-r1
-
-# Francois Bissey (kiwifb) (29 Oct 2010)
-# f.r.bissey@massey.ac.nz
-# mask paraview-3.8.* as there are no stable versions in the tree
-# Avoid accidental upgrade
->=sci-visualization/paraview-3.8.0
+# Justin Lecher <jlec@gentoo.org> (1 Aug 2009)
+# mask live ebuild
+=sci-chemistry/burrow-owl-9999_pre15
 
-# Andreas K. Huettel (dilfridge) (23 Jun 2010)
-# mask dev-lang/aldor for removal in 30d since there is no source available anymore
-# (was a svn checkout, but the server is dead)
-=dev-lang/aldor-1.1.0
+# Justin Lecher <jlec@gentoo.org> (08 Jun 2009)
+# mask live ebuilds
+=sci-chemistry/pymol-apbs-plugin-9999
+=sci-chemistry/coot-9999
+=sci-chemistry/pymol-9999
 
-# Andreas K. Huettel (dilfridge) (27 Jun 2010)
-# mask for removal in 30d since there is no source anymore
-# (fetch restricted, and the ftp server does not respond; no hint of program at HOMEPAGE)
-sci-biology/newbler
+# Justin Lecher <jlec@gentoo.org> (11 May 2009)
+# work in progress 
+=sci-chemistry/almost-1.0.3-r1

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

[Christoph Junghans]

commit:     3b0d5b6015b6bb6d3d7c5de3f0ca8e09d983280a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Jul 17 11:16:54 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Jul 17 11:16:54 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3b0d5b60

added votca-csg-tutorial to package.mask

---
 profiles/package.mask |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3e279a9..9efd7fd 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -85,6 +85,7 @@ sci-biology/tablet-bin
 # mask live ebuilds
 =sci-libs/votca-tools-9999
 =sci-chemistry/votca-csg-9999
+=sci-chemistry/votca-csg-tutorials-9999
 =app-doc/votca-csg-manual-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (02 Nov 2009)

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

[Christoph Junghans]

commit:     63c250bf35d852a83fc09c9f304953678b8ed212
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Jul 17 12:47:35 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Jul 17 12:47:35 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=63c250bf

added sci-chemistry/votca-csg-apps to package.mask

---
 profiles/package.mask |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9efd7fd..386ab9a 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -86,6 +86,7 @@ sci-biology/tablet-bin
 =sci-libs/votca-tools-9999
 =sci-chemistry/votca-csg-9999
 =sci-chemistry/votca-csg-tutorials-9999
+=sci-chemistry/votca-csg-apps-9999
 =app-doc/votca-csg-manual-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (02 Nov 2009)

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

[Kacper Kowalik]

commit:     c7379b1df44599c156589630ec3aff88b6a39946
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 23 17:29:25 2011 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Sat Jul 23 17:29:25 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c7379b1d

Addd package.use.mask. Mask dev-lang/path64[assembler]

---
 profiles/package.use.mask |   21 +++++++++++++++++++++
 1 files changed, 21 insertions(+), 0 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
new file mode 100644
index 0000000..f317d09
--- /dev/null
+++ b/profiles/package.use.mask
@@ -0,0 +1,21 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header$
+
+# When you add an entry to the top of this file, add your name, the date, and
+# an explanation of why something is getting masked. Please be extremely
+# careful not to commit atoms that are not valid, as it can cause large-scale
+# breakage, especially if it ends up in the daily snapshot.
+#
+## Example:
+##
+## # Dev E. Loper <developer@gentoo.org> (28 Jun 2012)
+## # Masking foo USE flag until we can get the
+## # foo stuff to work properly again (bug 12345)
+## =media-video/mplayer-0.90_pre5 foo
+## =media-video/mplayer-0.90_pre5-r1 foo
+#
+
+# Kacper Kowalik <xarthisius@gentoo.org> (23 Jul 2011)
+# mask assembler as it currently doesn't work
+dev-lang/path64 assembler

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

[Alexey Shvetsov]

commit:     34c97266699f7027c7f430d86e59855a2511e728
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 29 08:44:33 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Jul 29 08:44:33 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=34c97266

Mask live version of path64

---
 profiles/package.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 386ab9a..a736363 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Alexey Shvetsov <alexxy@gentoo.org> (30 Jul 2011)
+# Mask live version of path64
+~dev-lang/path64-9999
+
 # Justin Lecher <jlec@gentoo.org> (24 Jun 2011)
 # fftw dep is masked
 sci-libs/pfft

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

[Kacper Kowalik]

commit:     0029bff0ca07397d3318174a80213fa5a0003865
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 12 16:27:21 2011 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Fri Aug 12 16:27:21 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0029bff0

Fix categories

---
 profiles/categories |    5 ++++-
 1 files changed, 4 insertions(+), 1 deletions(-)

diff --git a/profiles/categories b/profiles/categories
index 964a77a..e1fb024 100644
--- a/profiles/categories
+++ b/profiles/categories
@@ -1,3 +1,5 @@
+app-admin
+app-benchmarks
 app-doc
 app-portage
 app-text
@@ -30,6 +32,7 @@ sci-physics
 sci-visualization
 sys-cluster
 sys-devel
-sys-infiniband
+sys-fs
+virtual
 www-apps
 x11-libs

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

[Kacper Kowalik]

commit:     e6011e079c76c71c643d1207246b44e2ae5bbf63
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 12 16:32:31 2011 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Fri Aug 12 16:32:31 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e6011e07

Update use.local.desc

---
 profiles/use.local.desc |  218 +++++++++++++++++++++++++++++++++--------------
 1 files changed, 152 insertions(+), 66 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index ea6b884..597e7df 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -1,74 +1,160 @@
-# Copyright 1999-2006 Gentoo Foundation.
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# This file is deprecated as per GLEP 56 in favor of metadata.xml. Please add
+# your descriptions to your package's metadata.xml ONLY.
+# * generated automatically using egencache *
 
-# This file contains descriptions of local USE flags, and the ebuilds which
-# contain them.
-# Keep it sorted.
-
-# We keep here only the new USE flags introduced by packages in the overlay.
-# Ultimately, they will be merged into the main tree.
-
-sci-biology/tgi-tools:pvm - Use sys-cluster/pvm (Parallel Virtual Machine) and build the pvmsx utility
-sci-chemistry/votca-csg:gromacs - Add support for gromacs file formats (sci-chemistry/gromacs)
-sci-geosciences/libtcd:non-commercial - Install tide constituent database that is free for non-commercial use only
+dev-java/hdf-java:hdf - Add support for the Hierarchical Data Format v.4 (sci-libs/hdf)
+dev-lang/icc:eclipse - Install the dev-util/eclipse-sdk plugins
+dev-lang/idb:eclipse - Install the dev-util/eclipse-sdk plugins
+dev-lang/path64:debugger - Build PathDB
+dev-lang/path64:native - Use EKOPath/Path64 for bootstraping
+dev-libs/intel-common:compiler - Install the libraries needed for the icc and ifort compilers
+dev-ml/mlgmpidl:mpfr - add support for mpfr, the library for multiple-precision floating-point computations with exact rounding
+dev-python/cvxopt:glpk - Use GNU Linear Programming Kit
+dev-python/ffnet:matplotlib - Use matplotlib for drawing
+media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled)
+net-misc/dhcp:client - Install the dhclient program
+net-misc/dhcp:infiniband - Enable ipoib support
+net-misc/dhcp:server - Install the dhcpd and dhcrelay programs
+sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
+sci-biology/estscan:intel - Use intel compiler
+sci-chemistry/avogadro:glsl - Enable glsl features via GLEW.
+sci-chemistry/gromacs:double-precision - More precise calculations at the expense of speed
+sci-chemistry/gromacs:fkernels - Enable building of Fortran Kernels for platforms that dont have assembly loops
+sci-chemistry/gromacs:single-precision - Single precision version of gromacs (default)
+sci-chemistry/jmol:client-only - Install the viewer only, no applet files for httpd
+sci-chemistry/pymol:apbs - Pymol supprt for sci-chemistry/apbs
+sci-chemistry/pymol:numpy - Enable numpy support for Pymol
+sci-chemistry/pymol:vmd - Builds molfile plugin support
+sci-chemistry/pymol:web - Install Pymodule needed for web app support
+sci-chemistry/rosetta:boinc - compile rosetta as a rosetta@home client
+sci-chemistry/rosetta:boost - compile rosetta with boost supported code
+sci-chemistry/votca-csg:boost - Compile against external boost headers from dev-libs/boost
+sci-chemistry/votca-csg:extras - Pull in extra applications from dev-libs/boost
+sci-chemistry/votca-csg:gromacs - Add support for gromacs file formats through sci-chemistry/gromacs
+sci-electronics/player:boost - Automatically generated description for boost
+sci-electronics/player:festival - Automatically generated description for festival
+sci-electronics/player:openssl - Automatically generated description for openssl
+sci-electronics/player:sphinx2 - Automatically generated description for sphinx2
+sci-geosciences/libtcd:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only.
+sci-geosciences/qgis:grass - Add support for sci-geosciences/grass
+sci-geosciences/xtide:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only.
+sci-libs/atlas:xblas - Build LAPACK with extra precision (needs sci-libs/xblas)
+sci-libs/bigdft:cuda - Add cuda support
 sci-libs/calculix-ccx:arpack - Add sparse eigen value support via sci-libs/arpack
-sci-libs/factory:singular - Add support for sci-mathematics/Singular
+sci-libs/factory:singular - Enable support for sci-mathematics/singular
+sci-libs/fox:dom - Automatically generated description for dom
+sci-libs/fox:fast - Automatically generated description for fast
+sci-libs/fox:sax - Automatically generated description for sax
+sci-libs/fox:wcml - Automatically generated description for wcml
+sci-libs/fox:wxml - Automatically generated description for wxml
 sci-libs/gmsh:cgns - Enables cgns output support
 sci-libs/gmsh:chaco - Enables chaco partitioner support
+sci-libs/gmsh:med - Enables med support
 sci-libs/gmsh:metis - Enables metis support
+sci-libs/gmsh:netgen - Enable 3D Frontal triangulation using netgen lib
 sci-libs/gmsh:opencascade - Enable OpenCASCADE support
-sci-libs/libfac:singular - Add support for sci-mathematics/Singular
+sci-libs/gmsh:petsc - Enable sci-mathematics/petsc support
+sci-libs/gmsh:taucs - Enable sci-libs/taucs support
+sci-libs/gmsh:tetgen - Enable 3D delauny triangulation using tetgen lib
+sci-libs/libcmatrix:atlas - Use of atlas blas implementation
+sci-libs/libfac:singular - Automatically generated description for singular
+sci-libs/lwpr:octave - Add sci-mathematics/octave support
+sci-libs/oasa:cairo - Add support for Cairo graphics library using dev-python/pycairo
+sci-libs/openblas:dynamic - Build dynamic architecture detection at run time (for multi targets)
+sci-libs/openblas:incblas - Build the CBLAS interface
+sci-libs/openblas:int64 - Build the 64 bits integer library
+sci-libs/openmm:cuda - Build Cuda lib
+sci-libs/openmm:opencl - Build OpenCL lib
+sci-libs/pagmo:kepler - Automatically generated description for kepler
+sci-libs/pagmo:nlopt - Automatically generated description for nlopt
 sci-libs/votca-tools:boost - Compile against external boost headers (dev-libs/boost)
-sci-mathematics/gap:xtom - extra tables of marks
+sci-libs/xdrfile:dmalloc - Enable use of Debug Malloc
+sci-mathematics/Macaulay2:optimization - Accept upstream's choices for -O option, i.e. -O3 almost everywhere.
+sci-mathematics/algae:intel - Use icc as c compiler
+sci-mathematics/apron:ppl - Enable optional interface to the Parma Polyhedra Library
+sci-mathematics/dolfin:cgal - Adds support for geometric algorithms with sci-mathematics/cgal
+sci-mathematics/dolfin:cholmod - Adds support for sparse Cholesky factorization with sci-libs/cholmod
+sci-mathematics/dolfin:parmetis - Adds support for parallel graph partitioning with sci-libs/parmetis
+sci-mathematics/dolfin:scotch - Adds support for graph partitioning with sci-libs/scotch
+sci-mathematics/dolfin:umfpack - Adds support for sparse solving with sci-libs/umfpack
+sci-mathematics/frama-c:apron - ?apron?
+sci-mathematics/frama-c:gtk - ?gtk?
+sci-mathematics/frama-c:why - ?why?
+sci-mathematics/gambit:X - Enable gui support using wxWidgets.
+sci-mathematics/gap:xtom - Automatically generated description for xtom
+sci-mathematics/giac:fltk - ?fltk?
 sci-mathematics/netgen:opencascade - Enable OpenCASCADE support
-sci-misc/opencascade:draw-harness - Enable building of draw-harness
-sci-misc/opencascade:stlport - Build OpenCASCADE with STLPort
-sci-misc/opencascade:wok - Enable building of WOK
-sci-misc/opennlp-tools:models - Install prebuild ME models (requires a ton of disk space)
-sci-misc/salome-component:openpbs - Enables openpbs support
-sci-misc/salome-gui:corba - Enables corba support
-sci-misc/salome-gui:glviewer - make glviewer module
-sci-misc/salome-gui:occviewer - make occviewer module
-sci-misc/salome-gui:plot2dviewer - make plot2dviewer module
-sci-misc/salome-gui:pyconsole - make python console module
-sci-misc/salome-gui:salomeobject - make salomeobject module
-sci-misc/salome-gui:supervgraphviewer - make supervgraphviewer module
-sci-misc/salome-gui:vtkviewer - make vtkviewer module
-sci-misc/salome-kernel:openpbs - Enables openpbs support
-sci-misc/salome-med:openpbs - Enables openpbs support
-sci-visualization/nodemon:pbs - Adds support for PBS (Portable Batch System) queries
-sys-cluster/openib-drivers:cxgb3 - make CXGB3 module
-sys-cluster/openib-drivers:ehca - make EHCA module
-sys-cluster/openib-drivers:hpage-patch - apply huge pages patch
-sys-cluster/openib-drivers:ipath - make IPATH module
-sys-cluster/openib-drivers:iser - make ISER module
-sys-cluster/openib-drivers:madeye - make MADEYE module
-sys-cluster/openib-drivers:memtrack - enable momory tracking
-sys-cluster/openib-drivers:mlx4 - make MLX4 module
-sys-cluster/openib-drivers:rds - make RDS module
-sys-cluster/openib-drivers:srp - make SRP module
-sys-cluster/openib-drivers:vnic - make VNIC module
-sys-cluster/openib-files:ehca - load EHCA module
-sys-cluster/openib-files:ipath - load IPATH module
-sys-cluster/openib-files:iser - load ISER module
-sys-cluster/openib-files:mlx4 - load MLX4 module
-sys-cluster/openib-files:rds - load RDS module
-sys-cluster/openib-files:srp - load SRP module
-sys-cluster/openib-files:vnic - load VNIC module
-sys-cluster/openib-mvapich2:large-cluster - build _LARGE_CLUSTER configuration
-sys-cluster/openib-mvapich2:medium-cluster - build _MEDIUM_CLUSTER configuration
-sys-cluster/openib-mvapich2:rdma - use rdmacm
-sys-cluster/openib-mvapich2:romio - enable ROMIO support
-sys-cluster/openib-userspace:cxgb3 - include libcxgb3 package
-sys-cluster/openib-userspace:dapl - add DAPL (Direct Access Provider Library) support
-sys-cluster/openib-userspace:ehca - include libehca package
-sys-cluster/openib-userspace:ipath - add PathScale HCA support
-sys-cluster/openib-userspace:mstflint - include mstflint package
-sys-cluster/openib-userspace:opensm - add OpenSM Subnet Management support.
-sys-cluster/openib-userspace:qlvnictools - include qlvnictools package
-sys-cluster/openib-userspace:srptools - include srptools package
-sys-cluster/openib-userspace:tvflash - include tvflash package
-sys-cluster/openib:dapl - add DAPL (Direct Access Provider Library) support.
-sys-cluster/openib:ipath - add PathScale HCA support.
-sys-cluster/openib:opensm - add OpenSM Subnet Management support.
+sci-mathematics/petsc:complex-scalars - Make scalars complex
+sci-mathematics/petsc:hypre - Use HYPRE (sci-mathematics/hypre) for preconditioning
+sci-mathematics/petsc:metis - Use METIS (sci-libs/parmetis) for partitioning
+sci-mathematics/polybori:sage - Replace the standard python interface by sage's python interface for easy integration in sage.
+sci-mathematics/scilab:gui - Build the Java base graphical interface
+sci-mathematics/scilab:matio - Enable support for MATLAB file through sci-libs/matio
+sci-mathematics/scilab:umfpack - Adds support for sparse solving with sci-libs/umfpack
+sci-mathematics/scilab:xcos - Enable building hybrid dynamic systems modeler and simulator Xcos
+sci-mathematics/why:apron - ?apron?
+sci-mathematics/why:coq - ?coq?
+sci-mathematics/why:gappa - ?gappa?
+sci-mathematics/why:gtk - ?gtk?
+sci-mathematics/why:jessie - ?jessie?
+sci-mathematics/why:pff - ?pff?
+sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-misc/openfst)
+sci-misc/hfst:sfst - Add optional support for sfst backend library (sci-misc/sfst)
+sci-misc/nco:ncap2 - Build next generation netcdf arithmetic processor (needs dev-java/antlr)
+sci-misc/nco:udunits - Add sci-libs/udunits files support
+sci-misc/opennlp-tools:models - Automatically generated description for models
+sci-misc/salome-kernel:numpy - Enable support for dev-python/numpy
+sci-misc/salome-med:metis - Add support for metis
+sci-misc/salome-med:scotch - Add support for scotch
+sci-physics/abinit:cuda - Enable support for nVidia CUDA
+sci-physics/abinit:fox - Enable support for FoX Fortran XML library
+sci-physics/abinit:vdwxc - Activate van der Waals exchange-correlation
+sci-physics/atompaw:libxc - Use libxc for something
+sci-physics/elk:libxc - Use sci-libs/libxc library of exchange-correlation functionals by ETSF.
+sci-physics/espresso:examples - Installs the examples
+sci-physics/espresso:packages - Installs extra subpackages
+sci-physics/fastjet:allcxxplugins - Build all C++ plugins.
+sci-physics/fastjet:allplugins - Build all standard plugins.
+sci-physics/fastjet:cgal - Use sci-mathematics/cgal instead of bundled algorithms.
+sci-physics/root:clarens - Buld the Clarens and PEAC plug-ins, to use in a GRID enabled analysis.
+sci-physics/root:fits - Support for images and data from FITS files with sci-libs/cfitsio
+sci-physics/root:llvm - Build the new cling interactive interpreter based on sys-devel/llvm
+sci-physics/root:math - Build all math related libraries plugins, needs sci-libs/gsl
+sci-physics/root:pythia6 - Builds the interface to Pythia-6 (sci-physics/pythia) high energy physics generation events library
+sci-physics/root:pythia8 - Builds the interface to Pythia-8 (sci-physics/pythia) high energy physics generation events library
+sci-physics/root:reflex - Builds the reflection database for the C++ interpretor
+sci-physics/root:xrootd - Build the xrootd low latency file server
+sci-visualization/gnuplot:gd - Add support for media-libs/gd. Needed for GIF, JPEG, and PNG image output.
+sci-visualization/gnuplot:qt4 - Build Qt4 terminal
+sci-visualization/gnuplot:thin-splines - Enable thin plate splines
+sci-visualization/nodemon:pbs - Enable support for the Portable Batch System.
+sci-visualization/paraview:adaptive - Enable the adaptive paraview application
+sci-visualization/paraview:cg - Add support for nvidia's cg shaders
+sci-visualization/paraview:coprocessing - Enable the coprocessing infrastructure which is mainly useful in the context of clusters
+sci-visualization/paraview:gui - Build paraview's gui not just the server
+sci-visualization/paraview:mysql - Build support for MySQL data item in the XDMF format
+sci-visualization/paraview:nvcontrol - Add NVCONTROL support for OpenGL options
+sci-visualization/paraview:plugins - Build and install additional plugins
+sci-visualization/paraview:streaming - Enable streaming paraview application
+sci-visualization/paraview:webkit - Built support for qt-webkit in vtk
+sci-visualization/v_sim:abinit - Add support for ABINIT file formats sci-physics/abinit
+sci-visualization/v_sim:cube - Add support plug-in support for Cube files (densities and structures)
+sci-visualization/v_sim:openbabel - Add support for ABINIT file formats sci-chemistry/openbabel
+sci-visualization/v_sim:xsf - plug-in support for files that follow the XCrysDen format for structural positions and densities
+sys-cluster/condor:classads - Enable the Condor's classified advertisement language
+sys-cluster/condor:drmaa - Enable the Distributed Resource Management Application API
+sys-cluster/condor:gcb - Enable condor to communicate over firewall/NAT
+sys-cluster/condor:kbdd - Enable the Condor Keyboard Daemon to monitor logged in X users for activity
+sys-cluster/mpich2:mpi-threads - Enable MPI_THREAD_MULTIPLE
+sys-cluster/mpich2:romio - Build the ROMIO MPI-IO component
+sys-cluster/mvapich2:large-cluster - Automatically generated description for large-cluster
+sys-cluster/mvapich2:medium-cluster - Automatically generated description for medium-cluster
+sys-cluster/mvapich2:romio - Automatically generated description for romio
+sys-cluster/openmpi:heterogeneous - Enable features required for heterogeneous platform support
+sys-cluster/openmpi:infiniband - Enable infiniband support
+sys-cluster/openmpi:mpi-threads - Enable MPI_THREAD_MULTIPLE
+sys-cluster/openmpi:pbs - Add support for the Portable Batch System (PBS)
+sys-cluster/openmpi:romio - Build the ROMIO MPI-IO component
+sys-cluster/openmpi:vt - Enable bundled VampirTrace support
+sys-fs/ocfs2-tools:external - Enable external locking
+virtual/mpi:romio - Enable romio, a high-performance portable MPI-IO

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

[Christoph Junghans]

commit:     b8374f134e3ece177c79ffd4699fe391bb540c99
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Aug 20 10:29:08 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Aug 20 10:29:08 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b8374f13

updated package.mask

---
 profiles/package.mask |    8 --------
 1 files changed, 0 insertions(+), 8 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 75cd9d3..9f67571 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -43,10 +43,6 @@
 ~dev-lang/path64-9999
 
 # Justin Lecher <jlec@gentoo.org> (24 Jun 2011)
-# fftw dep is masked
-sci-libs/pfft
-
-# Justin Lecher <jlec@gentoo.org> (24 Jun 2011)
 # paraview dep is masked
 sci-visualization/vtkPOFFReader
 
@@ -82,10 +78,6 @@ sci-biology/tablet-bin
 # masked for testing
 =sci-libs/openmm-2.0
 
-# Sebastien Fabbro (29 Sep 2010)
-# alpha software
->=sci-libs/fftw-3.3_alpha1
-
 # Christoph Junghans <ottxor@gentoo.org> (31 Jul 2010)
 # mask live ebuilds
 =sci-chemistry/gromacs-4.0.9999

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

[Justin Lecher]

commit:     69c14006b1d96d715a7f9c8f4507d0127f242e9c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 26 16:00:34 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Aug 26 16:00:34 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=69c14006

>sci-libs/blas-reference-20

---
 profiles/package.mask |    5 +++++
 1 files changed, 5 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index ff4e20f..07348dc 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,11 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher <jlec@gentoo.org> (26 Aug 2011)
+# Mask the tree reference-blas/lapack versions
+# resolves blas/lapack-eselect blocker, #380213
+>sci-libs/blas-reference-20
+
 # Dongxu Li <dongxuli2011@gmail.com> (10 Aug 2011)
 # Mask live version of librecad
 >=media-gfx/librecad-9999

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

[Justin Lecher]

commit:     4fd8b4ac091e33f522d5b24ca376985275dd5568
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 11 12:13:40 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Sep 11 12:13:40 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4fd8b4ac

removed unneeded entries to blas-reference

---
 profiles/package.mask |    4 ----
 1 files changed, 0 insertions(+), 4 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 07348dc..bee0fa6 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,10 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Justin Lecher <jlec@gentoo.org> (26 Aug 2011)
-# Mask the tree reference-blas/lapack versions
-# resolves blas/lapack-eselect blocker, #380213
->sci-libs/blas-reference-20
 
 # Dongxu Li <dongxuli2011@gmail.com> (10 Aug 2011)
 # Mask live version of librecad

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

[Christoph Junghans]

commit:     40cd1a764ac6f9d10562ae6105aec288946b2e09
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 28 07:15:42 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Sep 28 07:15:42 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=40cd1a76

updated package.mask

---
 profiles/package.mask |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index bee0fa6..3c550d8 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -88,6 +88,7 @@ sci-biology/tablet-bin
 # mask live ebuilds
 =sci-chemistry/gromacs-4.0.9999
 =sci-chemistry/gromacs-4.5.9999
+=sci-chemistry/gromacs-4.6.9999
 =sci-chemistry/gromacs-9999
 =app-doc/gromacs-manual-9999
 

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

[Justin Lecher]

commit:     1217c1276cca89056dc3d7e24b54337822f7f429
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 31 13:11:45 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Oct 31 13:11:45 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1217c127

Corrected email adress in ChangeLog entry

---
 profiles/package.mask |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3c550d8..6142833 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -61,7 +61,7 @@ sci-visualization/vtkPOFFReader
 # #348029
 sci-biology/tablet-bin
 
-# Sebastien Fabbro <ottxor@gentoo.org> (23 Aug 2011)
+# Sebastien Fabbro <bicatali@gentoo.org> (23 Aug 2011)
 # mask old blas from main tree to allow smoother transition to 
 # new blas/lapack framework
 =sci-libs/blas-reference-20070226*

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

[Christoph Junghans]

commit:     ea1b1193af4ece9b4fea13bafc48d7b26cf6dfbf
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Nov  5 03:04:46 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Nov  5 03:04:46 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ea1b1193

updated package.mask

---
 profiles/package.mask |    5 ++++-
 1 files changed, 4 insertions(+), 1 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 6142833..0b0bee1 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -92,12 +92,15 @@ sci-biology/tablet-bin
 =sci-chemistry/gromacs-9999
 =app-doc/gromacs-manual-9999
 
-# Christoph Junghans <ottxor@gentoo.org> (23 Jan 2010)
+# Christoph Junghans <ottxor@gentoo.org> (04 Nov 2011)
 # mask live ebuilds
 =sci-libs/votca-tools-9999
 =sci-chemistry/votca-csg-9999
 =sci-chemistry/votca-csg-tutorials-9999
 =sci-chemistry/votca-csgapps-9999
+=sci-chemistry/votca-ctp-9999
+=sci-chemistry/votca-kmc-9999
+=sci-chemistry/votca-moo-9999
 =app-doc/votca-csg-manual-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (02 Nov 2009)

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

[Martin Mokrejs]

commit:     ca4febc995bff1718ef21744c6c7a285b916dd5f
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec  9 16:48:40 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec  9 16:48:40 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ca4febc9

sci-biology/tablet-bin: ebuild cleanup, version bump, #348029

---
 profiles/package.mask |   14 --------------
 1 files changed, 0 insertions(+), 14 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 0b0bee1..cc1b7bb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -47,20 +47,6 @@
 # paraview dep is masked
 sci-visualization/vtkPOFFReader
 
-# Justin Lecher <jlec@gentoo.org> (04 Jan 2011)
-# Masked for several QA reasons:
-# portage screams during processing this ebuild
-# Author uses @gentoo.org address, although not a dev
-# java pkg, but no java eclass used
-# containing python code, but no python eclass used
-# tries to act interactivally with the installer, which doesn't work
-# instead source should be processed unpacked
-# repoman usage is recommended, as Changelog and metadata.xml are missing
-# line wrap at 80-100 chars
-# DESCRIPTION does not need to include $PN
-# #348029
-sci-biology/tablet-bin
-
 # Sebastien Fabbro <bicatali@gentoo.org> (23 Aug 2011)
 # mask old blas from main tree to allow smoother transition to 
 # new blas/lapack framework

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

[Christoph Junghans]

commit:     9817646f3998385671077c7c50b51759ef11d552
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 27 03:22:31 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Fri Jan 27 03:22:31 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9817646f

updated package.mask

---
 profiles/package.mask |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index cc1b7bb..84c5683 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -91,9 +91,9 @@ sci-visualization/vtkPOFFReader
 
 # Christoph Junghans <ottxor@gentoo.org> (02 Nov 2009)
 # live cvs ebuild, deps changing constantly
-# report to bug #232363
 =sci-visualization/gnuplot-4.4.9999
-=sci-visualization/gnuplot-4.5.9999
+=sci-visualization/gnuplot-4.6.9999
+=sci-visualization/gnuplot-4.7.9999
 
 # Justin Lecher <jlec@gentoo.org> (1 Aug 2009)
 # mask live ebuild

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

[Justin Lecher]

commit:     57cf1a8206c84cd463e750fabe2a80281bb74674
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 20 14:29:56 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 20 14:29:56 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=57cf1a82

Mask all emboss and embassy packages from overlay

---
 profiles/package.mask |   19 +++++++++++++++++++
 1 files changed, 19 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 84c5683..821518f 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,25 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher <jlec@gentoo.org> (20 Feb 2012)
+# They are broken in one or the other way
+# Need to be bumped to emboss-6.4.0
+sci-biology/emboss::science
+sci-biology/embassy::science
+sci-biology/embassy-cbstools::science
+sci-biology/embassy-domainatrix::science
+sci-biology/embassy-domalign::science
+sci-biology/embassy-domsearch::science
+sci-biology/embassy-emnu::science
+sci-biology/embassy-esim4::science
+sci-biology/embassy-hmmer::science
+sci-biology/embassy-iprscan::science
+sci-biology/embassy-mse::science
+sci-biology/embassy-phylipnew::science
+sci-biology/embassy-signature::science
+sci-biology/embassy-structure::science
+sci-biology/embassy-topo::science
+sci-biology/embassy-vienna::science
 
 # Dongxu Li <dongxuli2011@gmail.com> (10 Aug 2011)
 # Mask live version of librecad

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

[Justin Lecher]

commit:     f1e4797281c617ddf315a19616f0d1c415e7a06e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 20 14:50:15 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 20 14:50:15 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f1e47972

Correct masking syntax

---
 profiles/package.mask |   61 ++++++++++++++++++++++++++++++++++++-------------
 1 files changed, 45 insertions(+), 16 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 821518f..1e80f64 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,22 +33,51 @@
 # Justin Lecher <jlec@gentoo.org> (20 Feb 2012)
 # They are broken in one or the other way
 # Need to be bumped to emboss-6.4.0
-sci-biology/emboss::science
-sci-biology/embassy::science
-sci-biology/embassy-cbstools::science
-sci-biology/embassy-domainatrix::science
-sci-biology/embassy-domalign::science
-sci-biology/embassy-domsearch::science
-sci-biology/embassy-emnu::science
-sci-biology/embassy-esim4::science
-sci-biology/embassy-hmmer::science
-sci-biology/embassy-iprscan::science
-sci-biology/embassy-mse::science
-sci-biology/embassy-phylipnew::science
-sci-biology/embassy-signature::science
-sci-biology/embassy-structure::science
-sci-biology/embassy-topo::science
-sci-biology/embassy-vienna::science
+=sci-biology/embassy-6.0.1
+=sci-biology/embassy-6.1.0
+=sci-biology/embassy-6.3.1
+=sci-biology/embassy-cbstools-1.0.0
+=sci-biology/embassy-cbstools-1.0.0-r1
+=sci-biology/embassy-cbstools-1.0.0-r3
+=sci-biology/embassy-domainatrix-0.1.0-r3
+=sci-biology/embassy-domainatrix-0.1.0-r4
+=sci-biology/embassy-domainatrix-0.1.0-r6
+=sci-biology/embassy-domalign-0.1.0-r3
+=sci-biology/embassy-domalign-0.1.0-r4
+=sci-biology/embassy-domalign-0.1.0-r5
+=sci-biology/embassy-domsearch-0.1.0-r3
+=sci-biology/embassy-domsearch-0.1.0-r4
+=sci-biology/embassy-domsearch-0.1.0-r5
+=sci-biology/embassy-emnu-1.05-r5
+=sci-biology/embassy-emnu-1.05-r6
+=sci-biology/embassy-emnu-1.05-r7
+=sci-biology/embassy-esim4-1.0.0-r5
+=sci-biology/embassy-esim4-1.0.0-r6
+=sci-biology/embassy-esim4-1.0.0-r7
+=sci-biology/embassy-hmmer-2.3.2-r2
+=sci-biology/embassy-hmmer-2.3.2-r3
+=sci-biology/embassy-hmmer-2.3.2-r4
+=sci-biology/embassy-iprscan-4.3.1
+=sci-biology/embassy-iprscan-4.3.1-r1
+=sci-biology/embassy-iprscan-4.3.1-r2
+=sci-biology/embassy-mse-1.0.0-r6
+=sci-biology/embassy-mse-1.0.0-r7
+=sci-biology/embassy-mse-3.0.0
+=sci-biology/embassy-phylipnew-3.67
+=sci-biology/embassy-phylipnew-3.68
+=sci-biology/embassy-phylipnew-3.69
+=sci-biology/embassy-signature-0.1.0-r3
+=sci-biology/embassy-signature-0.1.0-r4
+=sci-biology/embassy-signature-0.1.0-r5
+=sci-biology/embassy-structure-0.1.0-r3
+=sci-biology/embassy-structure-0.1.0-r4
+=sci-biology/embassy-structure-0.1.0-r5
+=sci-biology/embassy-topo-1.0.0-r5
+=sci-biology/embassy-topo-1.0.0-r6
+=sci-biology/embassy-topo-2.0.0
+=sci-biology/embassy-vienna-1.7.2
+=sci-biology/embassy-vienna-1.7.2-r1
+=sci-biology/embassy-vienna-1.7.2-r2
 
 # Dongxu Li <dongxuli2011@gmail.com> (10 Aug 2011)
 # Mask live version of librecad

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

[Justin Lecher]

commit:     1666809977e6e5173df187efa3bdb759585f0b98
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 27 07:58:14 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 27 07:58:14 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=16668099

Correct masking, thanks zmedico for help, bump EAPI to 4-python

---
 profiles/ChangeLog    |    7 +++++
 profiles/eapi         |    1 +
 profiles/package.mask |   63 ++++++++++++++-----------------------------------
 3 files changed, 26 insertions(+), 45 deletions(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
new file mode 100644
index 0000000..fc83fc4
--- /dev/null
+++ b/profiles/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for profile directory
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/profiles/ChangeLog,v 1.6253 2012/02/27 06:07:13 bicatali Exp $
+
+  27 Feb 2012; Justin Lecher <jlec@gentoo.org> +eapi, package.mask:
+  Correct masking, thanks zmedico for help, bump EAPI to 4-python
+

diff --git a/profiles/eapi b/profiles/eapi
new file mode 100644
index 0000000..949c790
--- /dev/null
+++ b/profiles/eapi
@@ -0,0 +1 @@
+4-python

diff --git a/profiles/package.mask b/profiles/package.mask
index 1e80f64..2bef4c4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,51 +33,24 @@
 # Justin Lecher <jlec@gentoo.org> (20 Feb 2012)
 # They are broken in one or the other way
 # Need to be bumped to emboss-6.4.0
-=sci-biology/embassy-6.0.1
-=sci-biology/embassy-6.1.0
-=sci-biology/embassy-6.3.1
-=sci-biology/embassy-cbstools-1.0.0
-=sci-biology/embassy-cbstools-1.0.0-r1
-=sci-biology/embassy-cbstools-1.0.0-r3
-=sci-biology/embassy-domainatrix-0.1.0-r3
-=sci-biology/embassy-domainatrix-0.1.0-r4
-=sci-biology/embassy-domainatrix-0.1.0-r6
-=sci-biology/embassy-domalign-0.1.0-r3
-=sci-biology/embassy-domalign-0.1.0-r4
-=sci-biology/embassy-domalign-0.1.0-r5
-=sci-biology/embassy-domsearch-0.1.0-r3
-=sci-biology/embassy-domsearch-0.1.0-r4
-=sci-biology/embassy-domsearch-0.1.0-r5
-=sci-biology/embassy-emnu-1.05-r5
-=sci-biology/embassy-emnu-1.05-r6
-=sci-biology/embassy-emnu-1.05-r7
-=sci-biology/embassy-esim4-1.0.0-r5
-=sci-biology/embassy-esim4-1.0.0-r6
-=sci-biology/embassy-esim4-1.0.0-r7
-=sci-biology/embassy-hmmer-2.3.2-r2
-=sci-biology/embassy-hmmer-2.3.2-r3
-=sci-biology/embassy-hmmer-2.3.2-r4
-=sci-biology/embassy-iprscan-4.3.1
-=sci-biology/embassy-iprscan-4.3.1-r1
-=sci-biology/embassy-iprscan-4.3.1-r2
-=sci-biology/embassy-mse-1.0.0-r6
-=sci-biology/embassy-mse-1.0.0-r7
-=sci-biology/embassy-mse-3.0.0
-=sci-biology/embassy-phylipnew-3.67
-=sci-biology/embassy-phylipnew-3.68
-=sci-biology/embassy-phylipnew-3.69
-=sci-biology/embassy-signature-0.1.0-r3
-=sci-biology/embassy-signature-0.1.0-r4
-=sci-biology/embassy-signature-0.1.0-r5
-=sci-biology/embassy-structure-0.1.0-r3
-=sci-biology/embassy-structure-0.1.0-r4
-=sci-biology/embassy-structure-0.1.0-r5
-=sci-biology/embassy-topo-1.0.0-r5
-=sci-biology/embassy-topo-1.0.0-r6
-=sci-biology/embassy-topo-2.0.0
-=sci-biology/embassy-vienna-1.7.2
-=sci-biology/embassy-vienna-1.7.2-r1
-=sci-biology/embassy-vienna-1.7.2-r2
+sci-biology/embassy
+sci-biology/embassy-cbstools
+sci-biology/embassy-domainatrix
+sci-biology/embassy-domalign
+sci-biology/embassy-domsearch
+sci-biology/embassy-emnu
+sci-biology/embassy-esim4
+sci-biology/embassy-hmmer
+sci-biology/embassy-iprscan
+sci-biology/embassy-memenew
+sci-biology/embassy-mira
+sci-biology/embassy-mse
+sci-biology/embassy-phylipnew
+sci-biology/embassy-signature
+sci-biology/embassy-structure
+sci-biology/embassy-topo
+sci-biology/embassy-vienna
+sci-biology/embassy-clustalomega
 
 # Dongxu Li <dongxuli2011@gmail.com> (10 Aug 2011)
 # Mask live version of librecad

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

[Justin Lecher]

commit:     d8c8182e54fc0df263430ce3e632641412cd355e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 27 08:01:24 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 27 08:01:24 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d8c8182e

Dropped eapi again, zmedico: you don't need EAPI 4-python, when the ::repo is implied rather than explicit; masked sci-bioligy/amboss as well

---
 profiles/ChangeLog |    6 +++++-
 profiles/eapi      |    1 -
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index fc83fc4..c887899 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for profile directory
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/profiles/ChangeLog,v 1.6253 2012/02/27 06:07:13 bicatali Exp $
+# $Header: $
+
+  27 Feb 2012; Justin Lecher <jlec@gentoo.org> -eapi, package.mask:
+  Dropped eapi again, zmedico: you don't need EAPI 4-python, when the ::repo is
+  implied rather than explicit; masked sci-bioligy/amboss as well
 
   27 Feb 2012; Justin Lecher <jlec@gentoo.org> +eapi, package.mask:
   Correct masking, thanks zmedico for help, bump EAPI to 4-python

diff --git a/profiles/eapi b/profiles/eapi
deleted file mode 100644
index 949c790..0000000
--- a/profiles/eapi
+++ /dev/null
@@ -1 +0,0 @@
-4-python

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

[Justin Lecher]

commit:     701c6a70fb3ebaad26cb18cf070d7be7d0e88d9b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 27 08:03:10 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 27 08:03:10 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=701c6a70

Commit package.mask as well, was missing in last commit

---
 profiles/package.mask |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 2bef4c4..16eb0b7 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,6 +33,7 @@
 # Justin Lecher <jlec@gentoo.org> (20 Feb 2012)
 # They are broken in one or the other way
 # Need to be bumped to emboss-6.4.0
+sci-biology/emboss
 sci-biology/embassy
 sci-biology/embassy-cbstools
 sci-biology/embassy-domainatrix

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

[Sebastien Fabbro]

commit:     470c679db16fc7da4905af3741f3981fad854260
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Mar 12 16:44:19 2012 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Mar 12 16:44:19 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=470c679d

masked parmetis-4

---
 profiles/ChangeLog    |    3 +++
 profiles/package.mask |    6 ++++++
 2 files changed, 9 insertions(+), 0 deletions(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index c887899..81e35a7 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Mar 2012; Sébastien Fabbro <bicatali@gentoo.org> package.mask:
+  masked parmetis-4
+
   27 Feb 2012; Justin Lecher <jlec@gentoo.org> -eapi, package.mask:
   Dropped eapi again, zmedico: you don't need EAPI 4-python, when the ::repo is
   implied rather than explicit; masked sci-bioligy/amboss as well

diff --git a/profiles/package.mask b/profiles/package.mask
index 16eb0b7..e7e6360 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,12 @@
 
 #--- END OF EXAMPLES ---
 
+
+# Sebasien Fabbro <bicatali@gentoo.org> (10 Mar 2012)
+# incompatible API with previous versions of metis (4)
+# masked until reverse depedencies are fixed
+>=sci-libs/parmetis-4
+
 # Justin Lecher <jlec@gentoo.org> (20 Feb 2012)
 # They are broken in one or the other way
 # Need to be bumped to emboss-6.4.0

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

[Andrea Arteaga]

commit:     4ed178962d55cb998243466811a2a5f83caf90c6
Author:     Andrea Arteaga <andyspiros <AT> gmail <DOT> com>
AuthorDate: Sun Apr  8 00:52:05 2012 +0000
Commit:     Andrea Arteaga <andyspiros <AT> gmail <DOT> com>
CommitDate: Sun Apr  8 00:52:05 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4ed17896

[sci-libs/trilinos] Masked for testing.

---
 profiles/package.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index e7e6360..3356bfd 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -31,6 +31,10 @@
 #--- END OF EXAMPLES ---
 
 
+# Andrea Arteaga <andyspiros@gmail.com> (8 Apr 2012)
+# Masked for testing
+sci-libs/trilinos
+
 # Sebasien Fabbro <bicatali@gentoo.org> (10 Mar 2012)
 # incompatible API with previous versions of metis (4)
 # masked until reverse depedencies are fixed

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

[Andrea Arteaga]

commit:     03c6e1bfb20d301479e72ff9f145d3f576f16613
Author:     Andrea Arteaga <andyspiros <AT> gmail <DOT> com>
AuthorDate: Sat Apr 21 23:49:53 2012 +0000
Commit:     Andrea Arteaga <andyspiros <AT> gmail <DOT> com>
CommitDate: Sat Apr 21 23:49:53 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=03c6e1bf

[sys-cluster/ovis] Masked for testing.

---
 profiles/package.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3356bfd..3a13b63 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -31,6 +31,10 @@
 #--- END OF EXAMPLES ---
 
 
+# Andrea Arteaga <andyspiros@gmail.com> (22 Apr 2012)
+# Masked for testing
+sys-cluster/ovis
+
 # Andrea Arteaga <andyspiros@gmail.com> (8 Apr 2012)
 # Masked for testing
 sci-libs/trilinos

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

[Justin Lecher]

commit:     12d9af0de54afb53163dbd2339c30c5c1827a079
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Apr 28 07:01:28 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Apr 28 07:01:28 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=12d9af0d

mask =sci-libs/mmdb-1.24.20111208, no pkg-confiles installed

---
 profiles/package.mask |    3 +++
 1 files changed, 3 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3a13b63..e40d1ad 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,9 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher <jlec@gentoo.org> (28 Apr 2012)
+# Doesn't install pkg-config files, which many packages rely on
+=sci-libs/mmdb-1.24.20111208
 
 # Andrea Arteaga <andyspiros@gmail.com> (22 Apr 2012)
 # Masked for testing

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

[Sebastien Fabbro]

commit:     72ab64036b939963f61c75c64fa33f08fee4caee
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue May 15 00:01:49 2012 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue May 15 00:01:49 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=72ab6403

masked scilab-5.4*

---
 profiles/ChangeLog    |    3 +++
 profiles/package.mask |    4 ++++
 2 files changed, 7 insertions(+), 0 deletions(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index 81e35a7..c7b2f56 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 May 2012; Sébastien Fabbro <bicatali@gentoo.org> package.mask:
+  masked scilab-5.4*
+
   12 Mar 2012; Sébastien Fabbro <bicatali@gentoo.org> package.mask:
   masked parmetis-4
 

diff --git a/profiles/package.mask b/profiles/package.mask
index e40d1ad..25bed50 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Sebastien Fabbro <bicatali@gentoo.org> (14 May 2012)
+# alpha version for testing
+>=sci-mathematics/scilab-5.3.99
+
 # Justin Lecher <jlec@gentoo.org> (28 Apr 2012)
 # Doesn't install pkg-config files, which many packages rely on
 =sci-libs/mmdb-1.24.20111208

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

[Justin Lecher]

commit:     095f6f725d58681d2c851c5e3d58309f403f09f0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May 19 08:41:19 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May 19 08:41:19 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=095f6f72

Mask >=sci-libs/arpack-96 to make overlay users to tester

---
 profiles/package.mask |    5 ++++-
 1 files changed, 4 insertions(+), 1 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index e40d1ad..e520b36 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,7 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
-# Justin Lecher <jlec@gentoo.org> (28 Apr 2012)
+# Justin Lecher <jlec@gentoo.org> (30 Apr 2012)
+# Make sci overlay user to tester.
+>=sci-libs/arpack-96
+
 # Doesn't install pkg-config files, which many packages rely on
 =sci-libs/mmdb-1.24.20111208
 

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

[Justin Lecher]

commit:     7b39a7bfa0a27a60fa40c31320cc5ae87ce93cbd
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May 22 18:35:00 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May 22 18:35:00 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7b39a7bf

Mask old version schema of ncbi-tools to make overlay user to be tester

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/package.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 6beed02..9631588 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher <jlec@gentoo.org> (22 May 2012)
+# Make sci overlay user to tester.
+>=sci-biology/ncbi-tools-20080302
+
 # Sebastien Fabbro <bicatali@gentoo.org> (14 May 2012)
 # alpha version for testing
 >=sci-mathematics/scilab-5.3.99

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

[Justin Lecher]

commit:     8da631a9b99949935690b6ae806d6668177bd2e0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun  3 15:05:07 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun  3 15:05:07 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8da631a9

Mask old dssp and make sci overlay user to tester

---
 profiles/package.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9631588..72c57ef 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -32,6 +32,10 @@
 
 # Justin Lecher <jlec@gentoo.org> (22 May 2012)
 # Make sci overlay user to tester.
+>=sci-chemistry/dssp-070831
+
+# Justin Lecher <jlec@gentoo.org> (22 May 2012)
+# Make sci overlay user to tester.
 >=sci-biology/ncbi-tools-20080302
 
 # Sebastien Fabbro <bicatali@gentoo.org> (14 May 2012)

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

[Justin Lecher]

commit:     93ed550a0f357a9fa6b5f1a994683d10145947ae
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 13 11:03:03 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 13 11:03:03 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=93ed550a

Masks moved to tree

---
 profiles/package.mask |   12 ------------
 1 files changed, 0 insertions(+), 12 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 72c57ef..25bed50 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,22 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
-# Justin Lecher <jlec@gentoo.org> (22 May 2012)
-# Make sci overlay user to tester.
->=sci-chemistry/dssp-070831
-
-# Justin Lecher <jlec@gentoo.org> (22 May 2012)
-# Make sci overlay user to tester.
->=sci-biology/ncbi-tools-20080302
-
 # Sebastien Fabbro <bicatali@gentoo.org> (14 May 2012)
 # alpha version for testing
 >=sci-mathematics/scilab-5.3.99
 
-# Justin Lecher <jlec@gentoo.org> (30 Apr 2012)
-# Make sci overlay user to tester.
->=sci-libs/arpack-96
-
 # Justin Lecher <jlec@gentoo.org> (28 Apr 2012)
 # Doesn't install pkg-config files, which many packages rely on
 =sci-libs/mmdb-1.24.20111208

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

[Christoph Junghans]

commit:     eb511956cb55cb594eac78d198e6158c89daa779
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 14 17:57:20 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Thu Jun 14 17:57:20 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=eb511956

masked dev-lang/ispc-9999

---
 profiles/package.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 25bed50..c777816 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Christoph Junghans <ottxor@gentoo.org> (14 May 2012)
+# live ebuild
+=dev-lang/ispc-9999
+
 # Sebastien Fabbro <bicatali@gentoo.org> (14 May 2012)
 # alpha version for testing
 >=sci-mathematics/scilab-5.3.99

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

[Sebastien Fabbro]

commit:     ec826d5cd2122d39d53204ecb6d5a55c1278605c
Author:     Sebastien Fabbro <sfabbro <AT> uvic <DOT> ca>
AuthorDate: Wed Jul  4 22:42:15 2012 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jul  4 22:42:15 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ec826d5c

Mask live ebuilds from sci-astronomy

---
 profiles/ChangeLog    |    3 +++
 profiles/package.mask |    9 +++++++++
 2 files changed, 12 insertions(+), 0 deletions(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index c7b2f56..7ee94c0 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> package.mask:
+  Mask live ebuilds from sci-astronomy
+
   15 May 2012; Sébastien Fabbro <bicatali@gentoo.org> package.mask:
   masked scilab-5.4*
 

diff --git a/profiles/package.mask b/profiles/package.mask
index c777816..cd2257a 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,15 @@
 
 #--- END OF EXAMPLES ---
 
+# Sebastien Fabbro <bicatali@gentoo.org> (04 July 2012)
+# live ebuilds
+=sci-astronomy/psfex-9999
+=sci-astronomy/scamp-9999
+=sci-astronomy/sextractor-9999
+=sci-astronomy/skymaker-9999
+=sci-astronomy/stuff-9999
+=sci-astronomy/swarp-9999
+
 # Christoph Junghans <ottxor@gentoo.org> (14 May 2012)
 # live ebuild
 =dev-lang/ispc-9999

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

[Nicolas Bock]

commit:     c721f5ca50883b7ecbdbfc14d33357b4e2e999c4
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Thu Jul  5 19:46:15 2012 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu Jul  5 19:46:15 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c721f5ca

Added package mask for live ebuild, sci-chemistry/freeon-9999.

---
 profiles/package.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index cd2257a..9f3aec3 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Nicolas Bock <nicolasbock@gmail.com> (05 July 2012)
+# live ebuild
+=sci-chemistry/freeon-9999
+
 # Sebastien Fabbro <bicatali@gentoo.org> (04 July 2012)
 # live ebuilds
 =sci-astronomy/psfex-9999

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

[Sebastien Fabbro]

commit:     151803d1b5f86d16fabbf6264b74ffb05d3cc184
Author:     Sebastien Fabbro <sfabbro <AT> uvic <DOT> ca>
AuthorDate: Mon Jul  9 23:46:59 2012 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jul  9 23:46:59 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=151803d1

more sci-astronomy live ebuild masking

---
 profiles/ChangeLog    |    3 +++
 profiles/package.mask |    4 ++++
 2 files changed, 7 insertions(+), 0 deletions(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index 7ee94c0..9759e42 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  09 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> package.mask:
+  more sci-astronomy live ebuild masking
+
   04 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> package.mask:
   Mask live ebuilds from sci-astronomy
 

diff --git a/profiles/package.mask b/profiles/package.mask
index 9f3aec3..936f5a1 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -36,12 +36,16 @@
 
 # Sebastien Fabbro <bicatali@gentoo.org> (04 July 2012)
 # live ebuilds
+=sci-astronomy/eye-9999
+=sci-astronomy/missfits-9999
 =sci-astronomy/psfex-9999
 =sci-astronomy/scamp-9999
 =sci-astronomy/sextractor-9999
 =sci-astronomy/skymaker-9999
+=sci-astronomy/stiff-9999
 =sci-astronomy/stuff-9999
 =sci-astronomy/swarp-9999
+=sci-astronomy/weightwatcher-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (14 May 2012)
 # live ebuild

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

[Christoph Junghans]

commit:     88a908365b04dde980433892298faf26d811eb7a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 25 01:15:06 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Jul 25 01:15:06 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=88a90836

package.mask: removed obsolete entries

---
 profiles/package.mask |    3 ---
 1 files changed, 0 insertions(+), 3 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 8af2172..4e5d129 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -152,9 +152,6 @@ sci-visualization/vtkPOFFReader
 =sci-chemistry/votca-csg-9999
 =sci-chemistry/votca-csg-tutorials-9999
 =sci-chemistry/votca-csgapps-9999
-=sci-chemistry/votca-ctp-9999
-=sci-chemistry/votca-kmc-9999
-=sci-chemistry/votca-moo-9999
 =app-doc/votca-csg-manual-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (02 Nov 2009)

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

[Justin Lecher]

commit:     84c0777b8a3a976394e27cacf03184b6e01ab0ab
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 30 08:38:57 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Aug 30 08:38:57 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=84c0777b

add empty files for pcheck

---
 profiles/profiles.desc |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/profiles/arch.list b/profiles/arch.list
new file mode 100644
index 0000000..e69de29

diff --git a/profiles/profiles.desc b/profiles/profiles.desc
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/profiles/profiles.desc
@@ -0,0 +1 @@
+

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

[Justin Lecher]

commit:     b509b68963ee95b18c81b76dc4ee102b1174365d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 31 07:42:05 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Aug 31 07:42:05 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b509b689

update descriptions

---
 profiles/use.local.desc |  120 +++++++++++++++++++++++++++++++++++------------
 1 files changed, 89 insertions(+), 31 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 597e7df..3193225 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -2,25 +2,48 @@
 # your descriptions to your package's metadata.xml ONLY.
 # * generated automatically using egencache *
 
+dev-cpp/eigen:adolc - Enable use for automatic differentiation using sci-libs/adolc
+dev-cpp/eigen:sparse - Enable use for extra sparse matrix with sci-libs/umfpack, sci-libs/cholmod, sci-libs/superlu and dev-cpp/sparsehash
 dev-java/hdf-java:hdf - Add support for the Hierarchical Data Format v.4 (sci-libs/hdf)
+dev-java/hdf-java:hdfview - Build a GUI viewer for all files supported in dev-java/hdf-java
+dev-java/jogl:cg - Enable NVidia Cg binding.
 dev-lang/icc:eclipse - Install the dev-util/eclipse-sdk plugins
 dev-lang/idb:eclipse - Install the dev-util/eclipse-sdk plugins
-dev-lang/path64:debugger - Build PathDB
+dev-lang/path64:assembler - Build PathAS assembler
+dev-lang/path64:debugger - Build PathDB debugger
 dev-lang/path64:native - Use EKOPath/Path64 for bootstraping
+dev-lang/path64:valgrind - Support compiler debugging with dev-util/valgrind
 dev-libs/intel-common:compiler - Install the libraries needed for the icc and ifort compilers
 dev-ml/mlgmpidl:mpfr - add support for mpfr, the library for multiple-precision floating-point computations with exact rounding
-dev-python/cvxopt:glpk - Use GNU Linear Programming Kit
+dev-ml/zarith:mpir - Use mpir library instead of gmp
 dev-python/ffnet:matplotlib - Use matplotlib for drawing
+dev-python/pyhdf:szip - Allow to use sci-libs/szip for SZIP compression method in SDsetcompress()
+dev-util/nvidia-cuda-sdk:cuda - Build CUDA binaries
+dev-util/nvidia-cuda-sdk:opencl - Build OpenCL binaries
+dev-util/nvidia-cuda-toolkit:debugger - Installs the NVIDIA CUDA debugger
+dev-util/nvidia-cuda-toolkit:profiler - Installs the NVIDIA CUDA visual profiler
 media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled)
+net-fs/cvmfs:client - Install the cvmfs client programs and init script
+net-fs/cvmfs:server - Install the cvmfsd program and init script
 net-misc/dhcp:client - Install the dhclient program
-net-misc/dhcp:infiniband - Enable ipoib support
 net-misc/dhcp:server - Install the dhcpd and dhcrelay programs
 sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
-sci-biology/estscan:intel - Use intel compiler
+sci-astronomy/scamp:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
+sci-astronomy/sextractor:modelfit - Enable profile model fitting, needs sci-libs/atlas and sci-libs/fftw
+sci-astronomy/zpeg:gdl - Install GDL/IDL plotting routines
 sci-chemistry/avogadro:glsl - Enable glsl features via GLEW.
+sci-chemistry/ball:cuda - Include cuda support
+sci-chemistry/ball:sql - Include SQL database support
+sci-chemistry/ball:webkit - Uses x11-libs/qt-webkit for drawing
+sci-chemistry/gromacs:avx128fma - Enable 128bit avx with fma (e.g. AMD BullDozer)
+sci-chemistry/gromacs:avx256 - Enable 256bit avx (e.g. Intel Sandy Bridge)
+sci-chemistry/gromacs:cuda - Enable cuda non-bonded kernels
 sci-chemistry/gromacs:double-precision - More precise calculations at the expense of speed
 sci-chemistry/gromacs:fkernels - Enable building of Fortran Kernels for platforms that dont have assembly loops
+sci-chemistry/gromacs:hybrid - Enable hybrid acceleration kernels
+sci-chemistry/gromacs:power6 - Enable Power6 optimizations
 sci-chemistry/gromacs:single-precision - Single precision version of gromacs (default)
+sci-chemistry/gromacs:sse41 - Enable sse4.1 acceleration
 sci-chemistry/jmol:client-only - Install the viewer only, no applet files for httpd
 sci-chemistry/pymol:apbs - Pymol supprt for sci-chemistry/apbs
 sci-chemistry/pymol:numpy - Enable numpy support for Pymol
@@ -28,8 +51,7 @@ sci-chemistry/pymol:vmd - Builds molfile plugin support
 sci-chemistry/pymol:web - Install Pymodule needed for web app support
 sci-chemistry/rosetta:boinc - compile rosetta as a rosetta@home client
 sci-chemistry/rosetta:boost - compile rosetta with boost supported code
-sci-chemistry/votca-csg:boost - Compile against external boost headers from dev-libs/boost
-sci-chemistry/votca-csg:extras - Pull in extra applications from dev-libs/boost
+sci-chemistry/votca-csg:extras - Pull in extra applications from sci-chemistry/votca-csg-apps
 sci-chemistry/votca-csg:gromacs - Add support for gromacs file formats through sci-chemistry/gromacs
 sci-electronics/player:boost - Automatically generated description for boost
 sci-electronics/player:festival - Automatically generated description for festival
@@ -38,15 +60,30 @@ sci-electronics/player:sphinx2 - Automatically generated description for sphinx2
 sci-geosciences/libtcd:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only.
 sci-geosciences/qgis:grass - Add support for sci-geosciences/grass
 sci-geosciences/xtide:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only.
-sci-libs/atlas:xblas - Build LAPACK with extra precision (needs sci-libs/xblas)
+sci-libs/acml:gfortran - Fetch and install acml compiled with GNU FORTRAN compiler
+sci-libs/acml:ifort - Fetch and install acml compiled with the Intel FORTRAN compiler
+sci-libs/acml:int64 - Install the 64 bits integer library
+sci-libs/acml:nag - Fetch and install acml compiled with the NAG FORTRAN compiler
+sci-libs/acml:open64 - Fetch and install acml compiled with the Open64 FORTRAN Compiler
+sci-libs/acml:pgi - Fetch and install acml compiled with the Portland Group FORTRAN compiler
+sci-libs/armadillo:atlas - Link with ATLAS libraries for cblas and clapack (needs sci-libs/lapack-atlas)
+sci-libs/atlas:generic - Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)
 sci-libs/bigdft:cuda - Add cuda support
 sci-libs/calculix-ccx:arpack - Add sparse eigen value support via sci-libs/arpack
+sci-libs/coinor-clp:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
+sci-libs/coinor-clp:metis - Enable partitioning with sci-libs/metis
+sci-libs/coinor-clp:mumps - Enable sci-libs/mumps support
+sci-libs/coinor-clp:sparse - Enable support for sparse matrix with sci-libs/cholmod
+sci-libs/coinor-osi:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
+sci-libs/coinor-symphony:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
+sci-libs/coinor-utils:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
 sci-libs/factory:singular - Enable support for sci-mathematics/singular
-sci-libs/fox:dom - Automatically generated description for dom
-sci-libs/fox:fast - Automatically generated description for fast
-sci-libs/fox:sax - Automatically generated description for sax
-sci-libs/fox:wcml - Automatically generated description for wcml
-sci-libs/fox:wxml - Automatically generated description for wxml
+sci-libs/fox:dom - Compile the W3C document object model module
+sci-libs/fox:fast - Compile with best known optimization flags
+sci-libs/fox:sax - Compile the streaming, validating parser based on java's Simple API for XML
+sci-libs/fox:wcml - Compile the module for a subset of the Chemical Markup Language
+sci-libs/fox:wkml - Compile the module for the creation of KML documents used by applications such as Google Earth
+sci-libs/fox:wxml - Compile the XML writer used to sequentially create arbitrary XML documents quickly with minimal memory requirements
 sci-libs/gmsh:cgns - Enables cgns output support
 sci-libs/gmsh:chaco - Enables chaco partitioner support
 sci-libs/gmsh:med - Enables med support
@@ -56,19 +93,27 @@ sci-libs/gmsh:opencascade - Enable OpenCASCADE support
 sci-libs/gmsh:petsc - Enable sci-mathematics/petsc support
 sci-libs/gmsh:taucs - Enable sci-libs/taucs support
 sci-libs/gmsh:tetgen - Enable 3D delauny triangulation using tetgen lib
-sci-libs/libcmatrix:atlas - Use of atlas blas implementation
+sci-libs/gotoblas2:dynamic - Build dynamic architecture detection at run time (for multi targets)
+sci-libs/gotoblas2:incblas - Build the CBLAS interface
+sci-libs/gotoblas2:int64 - Build the 64 bits integer library
+sci-libs/ipopt:mumps - Enable sci-libs/mumps support
+sci-libs/lapack-reference:xblas - Build LAPACK with extra precision (needs sci-libs/xblas)
+sci-libs/lapacke-reference:xblas - Build LAPACKE with extra precision (needs sci-libs/xblas)
+sci-libs/levmar:plasma - Use the multi-threaded sci-libs/plasma library for linear algebra
 sci-libs/libfac:singular - Automatically generated description for singular
 sci-libs/lwpr:octave - Add sci-mathematics/octave support
+sci-libs/magma:fermi - Compile for GPU NVIDIA Fermi family (2.x cards)
+sci-libs/magma:tesla - Compile for GPU NVIDIA Tesla family (1.x cards)>
+sci-libs/mumps:metis - Enable ordering with METIS (sci-libs/metis, sci-libs/parmetis)
+sci-libs/mumps:scotch - Enable ordering with sci-libs/scotch
 sci-libs/oasa:cairo - Add support for Cairo graphics library using dev-python/pycairo
 sci-libs/openblas:dynamic - Build dynamic architecture detection at run time (for multi targets)
 sci-libs/openblas:incblas - Build the CBLAS interface
 sci-libs/openblas:int64 - Build the 64 bits integer library
-sci-libs/openmm:cuda - Build Cuda lib
-sci-libs/openmm:opencl - Build OpenCL lib
 sci-libs/pagmo:kepler - Automatically generated description for kepler
 sci-libs/pagmo:nlopt - Automatically generated description for nlopt
-sci-libs/votca-tools:boost - Compile against external boost headers (dev-libs/boost)
-sci-libs/xdrfile:dmalloc - Enable use of Debug Malloc
+sci-libs/parmetis:double-precision - Floating-point operation done as double precision
+sci-libs/parmetis:int64 - Build the 64 bits integer library (needed for > 2^31 vertices)
 sci-mathematics/Macaulay2:optimization - Accept upstream's choices for -O option, i.e. -O3 almost everywhere.
 sci-mathematics/algae:intel - Use icc as c compiler
 sci-mathematics/apron:ppl - Enable optional interface to the Parma Polyhedra Library
@@ -83,11 +128,20 @@ sci-mathematics/frama-c:why - ?why?
 sci-mathematics/gambit:X - Enable gui support using wxWidgets.
 sci-mathematics/gap:xtom - Automatically generated description for xtom
 sci-mathematics/giac:fltk - ?fltk?
+sci-mathematics/htk:hdecode - Install HDecode, a large vocabulary word recogniser
+sci-mathematics/htk:hlmtools - Install the tools for manipulation of language models
+sci-mathematics/htk:hslab - Install HSLab a label editor for speech label manipulation
+sci-mathematics/htk:htkbook - Build the HTK documentation (HTK Book)
 sci-mathematics/netgen:opencascade - Enable OpenCASCADE support
+sci-mathematics/petsc:afterimage - Use Afterstep image library (media-libs/libafterimage)
 sci-mathematics/petsc:complex-scalars - Make scalars complex
-sci-mathematics/petsc:hypre - Use HYPRE (sci-mathematics/hypre) for preconditioning
+sci-mathematics/petsc:hypre - Use HYPRE (sci-mathematics/hypre) and for preconditioning
 sci-mathematics/petsc:metis - Use METIS (sci-libs/parmetis) for partitioning
-sci-mathematics/polybori:sage - Replace the standard python interface by sage's python interface for easy integration in sage.
+sci-mathematics/petsc:sparse - Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization
+sci-mathematics/petsc:superlu - Use superlu (sci-libs/superlu) for preconditioning
+sci-mathematics/polymake:libpolymake - Build the polymake library to build applications using the C++ interface.
+sci-mathematics/rstudio:desktop - Build the QT4 desktop interface
+sci-mathematics/rstudio:server - Build and install the RStudio server
 sci-mathematics/scilab:gui - Build the Java base graphical interface
 sci-mathematics/scilab:matio - Enable support for MATLAB file through sci-libs/matio
 sci-mathematics/scilab:umfpack - Adds support for sparse solving with sci-libs/umfpack
@@ -98,37 +152,42 @@ sci-mathematics/why:gappa - ?gappa?
 sci-mathematics/why:gtk - ?gtk?
 sci-mathematics/why:jessie - ?jessie?
 sci-mathematics/why:pff - ?pff?
+sci-misc/hfst:foma - Add optional support for foma backend library (sci-misc/foma)
+sci-misc/hfst:glib - Parse UTF-8 and collate unicode using glib instead of homebrewn methods
 sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-misc/openfst)
 sci-misc/hfst:sfst - Add optional support for sfst backend library (sci-misc/sfst)
-sci-misc/nco:ncap2 - Build next generation netcdf arithmetic processor (needs dev-java/antlr)
-sci-misc/nco:udunits - Add sci-libs/udunits files support
+sci-misc/hfst:xml - Include parsers for grammars and formats that require XML support
 sci-misc/opennlp-tools:models - Automatically generated description for models
 sci-misc/salome-kernel:numpy - Enable support for dev-python/numpy
 sci-misc/salome-med:metis - Add support for metis
 sci-misc/salome-med:scotch - Add support for scotch
 sci-physics/abinit:cuda - Enable support for nVidia CUDA
+sci-physics/abinit:cuda-double - Enable support for double precision nVidia CUDA
+sci-physics/abinit:fftw-threads - Use the threaded version of sci-libs/fftw
 sci-physics/abinit:fox - Enable support for FoX Fortran XML library
+sci-physics/abinit:gui - Build the abinit GUI (requires java)
+sci-physics/abinit:libabinit - Build the libabinit used by sci-libs/bigdft (usage not tested yet, circular dependency not resolved)
 sci-physics/abinit:vdwxc - Activate van der Waals exchange-correlation
 sci-physics/atompaw:libxc - Use libxc for something
 sci-physics/elk:libxc - Use sci-libs/libxc library of exchange-correlation functionals by ETSF.
 sci-physics/espresso:examples - Installs the examples
 sci-physics/espresso:packages - Installs extra subpackages
-sci-physics/fastjet:allcxxplugins - Build all C++ plugins.
-sci-physics/fastjet:allplugins - Build all standard plugins.
-sci-physics/fastjet:cgal - Use sci-mathematics/cgal instead of bundled algorithms.
-sci-physics/root:clarens - Buld the Clarens and PEAC plug-ins, to use in a GRID enabled analysis.
+sci-physics/root:c++0x - Build ROOT using the C++11 standard. Not supported, requires sys-devel/gcc>=4.7.0
 sci-physics/root:fits - Support for images and data from FITS files with sci-libs/cfitsio
+sci-physics/root:geocad - Enable ROOT-CAD interface using sci-libs/opencascade
+sci-physics/root:htmldoc - Generate html documentation
 sci-physics/root:llvm - Build the new cling interactive interpreter based on sys-devel/llvm
 sci-physics/root:math - Build all math related libraries plugins, needs sci-libs/gsl
-sci-physics/root:pythia6 - Builds the interface to Pythia-6 (sci-physics/pythia) high energy physics generation events library
-sci-physics/root:pythia8 - Builds the interface to Pythia-8 (sci-physics/pythia) high energy physics generation events library
-sci-physics/root:reflex - Builds the reflection database for the C++ interpretor
-sci-physics/root:xrootd - Build the xrootd low latency file server
+sci-physics/root:pythia6 - Build the interface for sci-physics/pythia version 6.x
+sci-physics/root:pythia8 - Build the interface for sci-physics/pythia version 8.x
+sci-physics/root:reflex - Build the reflection database for the C++ interpreter
+sci-physics/root:xrootd - Build the interface for net-libs/xrootd
+sci-visualization/gnuplot:bitmap - Enable dot-matrix printers and pbm terminal
 sci-visualization/gnuplot:gd - Add support for media-libs/gd. Needed for GIF, JPEG, and PNG image output.
-sci-visualization/gnuplot:qt4 - Build Qt4 terminal
 sci-visualization/gnuplot:thin-splines - Enable thin plate splines
 sci-visualization/nodemon:pbs - Enable support for the Portable Batch System.
 sci-visualization/paraview:adaptive - Enable the adaptive paraview application
+sci-visualization/paraview:boost - Add support for boost
 sci-visualization/paraview:cg - Add support for nvidia's cg shaders
 sci-visualization/paraview:coprocessing - Enable the coprocessing infrastructure which is mainly useful in the context of clusters
 sci-visualization/paraview:gui - Build paraview's gui not just the server
@@ -156,5 +215,4 @@ sys-cluster/openmpi:mpi-threads - Enable MPI_THREAD_MULTIPLE
 sys-cluster/openmpi:pbs - Add support for the Portable Batch System (PBS)
 sys-cluster/openmpi:romio - Build the ROMIO MPI-IO component
 sys-cluster/openmpi:vt - Enable bundled VampirTrace support
-sys-fs/ocfs2-tools:external - Enable external locking
 virtual/mpi:romio - Enable romio, a high-performance portable MPI-IO

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

[Christoph Junghans]

commit:     0faececf69cec8297242efc44bac40f8421a417d
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Oct  4 04:13:38 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Thu Oct  4 04:13:38 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0faececf

updated package.mask

---
 profiles/package.mask |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 4bb34d8..b1714bc 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -143,6 +143,7 @@ sci-visualization/vtkPOFFReader
 =sci-chemistry/gromacs-4.5.9999
 =sci-chemistry/gromacs-4.6.9999
 =sci-chemistry/gromacs-9999
+=app-doc/gromacs-manual-4.6.9999
 =app-doc/gromacs-manual-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (04 Nov 2011)

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

[Justin Lecher]

commit:     dd0fbc75836507bbd3e3ff67e04c190ac6432611
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 10 05:39:13 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 10 05:39:13 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dd0fbc75

dummy files added to make pcheck happy

---
 0 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/profiles/arch.list b/profiles/arch.list
new file mode 100644
index 0000000..e69de29

diff --git a/profiles/profiles.desc b/profiles/profiles.desc
new file mode 100644
index 0000000..e69de29

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

[Christoph Junghans]

commit:     ac355c4620dc28e40f5d1c2ab6069d68656fd77b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Oct  9 12:52:44 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Tue Oct  9 12:52:44 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ac355c46

package.mask: added sci-physics/espresso++

---
 profiles/package.mask |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index b1714bc..9953a7d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -122,6 +122,7 @@ sci-visualization/vtkPOFFReader
 # Christoph Junghans <ottxor@gentoo.org> (20 Apr 2011)
 # mask live ebuild
 =sci-physics/espresso-9999
+=sci-physics/espresso++-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (23 Jan 2011)
 # mask live ebuild

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

[Christoph Junghans]

commit:     197f72bc8fb6d327b89bab6342429975f04a9c8c
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 27 05:21:36 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Tue Nov 27 05:28:48 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=197f72bc

mask sci-chemistry/gromacs[openmm]

---
 profiles/package.use.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index f317d09..87b7671 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -19,3 +19,7 @@
 # Kacper Kowalik <xarthisius@gentoo.org> (23 Jul 2011)
 # mask assembler as it currently doesn't work
 dev-lang/path64 assembler
+
+# Christoph Junghans <ottoxr@gentoo.org> (26 Nov 2012)
+# openmm is still under testing
+sci-chemistry/gromacs openmm

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

[Christoph Junghans]

commit:     93adeb11bb25a0bb28fb28250d986979261cddc5
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 30 21:07:22 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Fri Nov 30 21:07:22 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=93adeb11

moved to gx86 profile

---
 profiles/package.use.mask |    4 ----
 1 files changed, 0 insertions(+), 4 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 87b7671..f317d09 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -19,7 +19,3 @@
 # Kacper Kowalik <xarthisius@gentoo.org> (23 Jul 2011)
 # mask assembler as it currently doesn't work
 dev-lang/path64 assembler
-
-# Christoph Junghans <ottoxr@gentoo.org> (26 Nov 2012)
-# openmm is still under testing
-sci-chemistry/gromacs openmm

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

[Christoph Junghans]

commit:     b0f2bea18578b3749fe5cb1c49c87146468ff46f
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 27 21:34:51 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Thu Dec 27 21:42:38 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b0f2bea1

masked dev-util/ccache use flags

---
 profiles/package.use.mask |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index f317d09..0bd0cfa 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -16,6 +16,10 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
+# Christoph Junghans <ottxor@gentoo.org> (27 Dec 2012)
+# icc/clang is not supported by all platforms
+dev-util/ccache icc clang
+
 # Kacper Kowalik <xarthisius@gentoo.org> (23 Jul 2011)
 # mask assembler as it currently doesn't work
 dev-lang/path64 assembler

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

[Guillaume Horel]

commit:     05d62bd1bfeb7095f2dedeb9f0c25b331e56483f
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Tue Jan 29 03:49:58 2013 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Tue Jan 29 03:49:58 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=05d62bd1

unmask scilab-5.4

---
 profiles/package.mask |    7 -------
 1 files changed, 0 insertions(+), 7 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9953a7d..5c8ce2c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,13 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Guillaume Horel <guillaume.horel@gmail.com> (11 July 2012)
-# masked for upcoming scilab-5.4.0
-=sci-mathematics/scilab-5.4.0
-=dev-java/jrosetta-1.0.4
-=dev-java/flexdock-1.2.0
->=dev-java/jgraphx-1.8
-
 # Nicolas Bock <nicolasbock@gmail.com> (05 July 2012)
 # live ebuild
 =sci-chemistry/freeon-9999

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

[Christoph Junghans]

commit:     63f832c6e530b4ef9c8760be7d414167fd1906b9
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Feb  2 00:48:09 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Feb  2 00:48:09 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=63f832c6

clean up package.mask

---
 profiles/package.mask |   10 ----------
 1 files changed, 0 insertions(+), 10 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 5c8ce2c..094b0dc 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -127,30 +127,20 @@ sci-visualization/vtkPOFFReader
 # Avoid accidental upgrade
 >=sci-visualization/paraview-3.8.0
 
-# Christoph Junghans <ottxor@gentoo.org> (03 Oct 2010)
-# masked for testing
-=sci-libs/openmm-2.0
-
 # Christoph Junghans <ottxor@gentoo.org> (31 Jul 2010)
 # mask live ebuilds
-=sci-chemistry/gromacs-4.0.9999
 =sci-chemistry/gromacs-4.5.9999
 =sci-chemistry/gromacs-4.6.9999
 =sci-chemistry/gromacs-9999
-=app-doc/gromacs-manual-4.6.9999
-=app-doc/gromacs-manual-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (04 Nov 2011)
 # mask live ebuilds
 =sci-libs/votca-tools-9999
 =sci-chemistry/votca-csg-9999
-=sci-chemistry/votca-csg-tutorials-9999
 =sci-chemistry/votca-csgapps-9999
-=app-doc/votca-csg-manual-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (02 Nov 2009)
 # live cvs ebuild, deps changing constantly
-=sci-visualization/gnuplot-4.4.9999
 =sci-visualization/gnuplot-4.6.9999
 =sci-visualization/gnuplot-4.7.9999
 

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

[Justin Lecher]

commit:     067f3bb349886c2c44e8829b0d4a75e73c7f0746
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  3 17:47:25 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  3 17:47:25 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=067f3bb3

Mask several package due to different QA issues

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/package.mask |   12 ++++++++++++
 1 files changed, 12 insertions(+), 0 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 094b0dc..1c816ac 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,18 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher <jlec@gentoo.org> (03 March 2013)
+# Mask for missing license
+sci-biology/lastz
+sci-biology/phylobayes
+
+# Justin Lecher <jlec@gentoo.org> (03 March 2013)
+# Missing deps
+sci-biology/gbrowse
+sci-mathematics/surfer
+dev-python/pymvpa
+sci-biology/artemis-bin
+
 # Nicolas Bock <nicolasbock@gmail.com> (05 July 2012)
 # live ebuild
 =sci-chemistry/freeon-9999

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

[Justin Lecher]

commit:     ae1053378761c62e5f0a91d1437b7d37d3c1e303
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 12 19:28:14 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 12 19:28:14 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ae105337

Merge live ebuilds on top
drop unversioned "mask for testing"
drop obsolete
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/package.mask | 113 ++++++++++++++------------------------------------
 1 file changed, 32 insertions(+), 81 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1c816ac..05296c8 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,10 +30,38 @@
 
 #--- END OF EXAMPLES ---
 
-# Justin Lecher <jlec@gentoo.org> (03 March 2013)
-# Mask for missing license
-sci-biology/lastz
-sci-biology/phylobayes
+# Live ebuilds go here
+# keep this on top
+>=sci-chemistry/freeon-9999
+>=sci-astronomy/eye-9999
+>=sci-astronomy/missfits-9999
+>=sci-astronomy/psfex-9999
+>=sci-astronomy/scamp-9999
+>=sci-astronomy/sextractor-9999
+>=sci-astronomy/skymaker-9999
+>=sci-astronomy/stiff-9999
+>=sci-astronomy/stuff-9999
+>=sci-astronomy/swarp-9999
+>=sci-astronomy/weightwatcher-9999
+>=dev-lang/ispc-9999
+>=media-gfx/librecad-9999
+>=media-gfx/brlcad-9999
+>=dev-lang/path64-9999
+>=sys-cluster/nullmpi-9999
+>=sci-physics/espresso-9999
+>=sci-physics/espresso++-9999
+>=sci-chemistry/gromacs-4.5.9999
+>=sci-chemistry/gromacs-4.6.9999
+>=sci-chemistry/gromacs-9999
+>=sci-libs/votca-tools-9999
+>=sci-chemistry/votca-csg-9999
+>=sci-chemistry/votca-csgapps-9999
+~sci-visualization/gnuplot-4.6.9999
+~sci-visualization/gnuplot-4.7.9999
+~sci-chemistry/burrow-owl-9999_pre15
+>=sci-chemistry/pymol-apbs-plugin-9999
+>=sci-chemistry/coot-9999
+>=sci-chemistry/pymol-9999
 
 # Justin Lecher <jlec@gentoo.org> (03 March 2013)
 # Missing deps
@@ -42,39 +70,10 @@ sci-mathematics/surfer
 dev-python/pymvpa
 sci-biology/artemis-bin
 
-# Nicolas Bock <nicolasbock@gmail.com> (05 July 2012)
-# live ebuild
-=sci-chemistry/freeon-9999
-
-# Sebastien Fabbro <bicatali@gentoo.org> (04 July 2012)
-# live ebuilds
-=sci-astronomy/eye-9999
-=sci-astronomy/missfits-9999
-=sci-astronomy/psfex-9999
-=sci-astronomy/scamp-9999
-=sci-astronomy/sextractor-9999
-=sci-astronomy/skymaker-9999
-=sci-astronomy/stiff-9999
-=sci-astronomy/stuff-9999
-=sci-astronomy/swarp-9999
-=sci-astronomy/weightwatcher-9999
-
-# Christoph Junghans <ottxor@gentoo.org> (14 May 2012)
-# live ebuild
-=dev-lang/ispc-9999
-
 # Justin Lecher <jlec@gentoo.org> (28 Apr 2012)
 # Doesn't install pkg-config files, which many packages rely on
 =sci-libs/mmdb-1.24.20111208
 
-# Andrea Arteaga <andyspiros@gmail.com> (22 Apr 2012)
-# Masked for testing
-sys-cluster/ovis
-
-# Andrea Arteaga <andyspiros@gmail.com> (8 Apr 2012)
-# Masked for testing
-sci-libs/trilinos
-
 # Sebasien Fabbro <bicatali@gentoo.org> (10 Mar 2012)
 # incompatible API with previous versions of metis (4)
 # masked until reverse depedencies are fixed
@@ -103,18 +102,6 @@ sci-biology/embassy-topo
 sci-biology/embassy-vienna
 sci-biology/embassy-clustalomega
 
-# Dongxu Li <dongxuli2011@gmail.com> (10 Aug 2011)
-# Mask live version of librecad
->=media-gfx/librecad-9999
-
-# Dongxu Li <dongxuli2011@gmail.com> (10 Aug 2011)
-# Mask live version of brlcad
->=media-gfx/brlcad-9999
-
-# Alexey Shvetsov <alexxy@gentoo.org> (30 Jul 2011)
-# Mask live version of path64
-~dev-lang/path64-9999
-
 # Justin Lecher <jlec@gentoo.org> (24 Jun 2011)
 # paraview dep is masked
 sci-visualization/vtkPOFFReader
@@ -124,48 +111,12 @@ sci-visualization/vtkPOFFReader
 # new blas/lapack framework
 =sci-libs/blas-reference-20070226*
 
-# Christoph Junghans <ottxor@gentoo.org> (20 Apr 2011)
-# mask live ebuild
-=sci-physics/espresso-9999
-=sci-physics/espresso++-9999
-
-# Christoph Junghans <ottxor@gentoo.org> (23 Jan 2011)
-# mask live ebuild
-=sys-cluster/nullmpi-9999
-
 # Francois Bissey (kiwifb) (29 Oct 2010)
 # f.r.bissey@massey.ac.nz
 # mask paraview-3.8.* as there are no stable versions in the tree
 # Avoid accidental upgrade
 >=sci-visualization/paraview-3.8.0
 
-# Christoph Junghans <ottxor@gentoo.org> (31 Jul 2010)
-# mask live ebuilds
-=sci-chemistry/gromacs-4.5.9999
-=sci-chemistry/gromacs-4.6.9999
-=sci-chemistry/gromacs-9999
-
-# Christoph Junghans <ottxor@gentoo.org> (04 Nov 2011)
-# mask live ebuilds
-=sci-libs/votca-tools-9999
-=sci-chemistry/votca-csg-9999
-=sci-chemistry/votca-csgapps-9999
-
-# Christoph Junghans <ottxor@gentoo.org> (02 Nov 2009)
-# live cvs ebuild, deps changing constantly
-=sci-visualization/gnuplot-4.6.9999
-=sci-visualization/gnuplot-4.7.9999
-
-# Justin Lecher <jlec@gentoo.org> (1 Aug 2009)
-# mask live ebuild
-=sci-chemistry/burrow-owl-9999_pre15
-
-# Justin Lecher <jlec@gentoo.org> (08 Jun 2009)
-# mask live ebuilds
-=sci-chemistry/pymol-apbs-plugin-9999
-=sci-chemistry/coot-9999
-=sci-chemistry/pymol-9999
-
 # Justin Lecher <jlec@gentoo.org> (11 May 2009)
 # work in progress 
 =sci-chemistry/almost-1.0.3-r1

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

[Justin Lecher]

commit:     42d3f4ecde751219923680af4a7f16f35847a4e0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 17 05:53:57 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 17 05:54:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=42d3f4ec

add missing masks for live ebuilds

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 05296c8..0c270df 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -32,6 +32,11 @@
 
 # Live ebuilds go here
 # keep this on top
+>=media-gfx/brlcad-9999
+>=dev-lang/path64-9999
+>=dev-lang/julia-9999
+>=dev-lang/ispc-9999
+>=app-benchmarks/btl-9999
 >=sci-chemistry/freeon-9999
 >=sci-astronomy/eye-9999
 >=sci-astronomy/missfits-9999

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

[Christoph Junghans]

commit:     acbc588d0ee198e6a95a3369e9b439630332f992
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Jul  5 23:33:51 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jul  5 23:33:51 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=acbc588d

fixed package.mask for sci-chemistry/gromacs

---
 profiles/package.mask | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index f354cdf..4edd695 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -55,9 +55,9 @@
 >=sys-cluster/nullmpi-9999
 >=sci-physics/espresso-9999
 >=sci-physics/espresso++-9999
->=sci-chemistry/gromacs-4.5.9999
->=sci-chemistry/gromacs-4.6.9999
->=sci-chemistry/gromacs-9999
+~sci-chemistry/gromacs-4.5.9999
+~sci-chemistry/gromacs-4.6.9999
+~sci-chemistry/gromacs-9999
 >=sci-libs/votca-tools-9999
 >=sci-chemistry/votca-csg-9999
 >=sci-chemistry/votca-csgapps-9999

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

[Christoph Junghans]

commit:     a7e86ca2842e3eb09e1f53cc37056209a7285351
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Sep  1 19:50:07 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Sep  1 19:50:07 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a7e86ca2

updated package.mask

---
 profiles/package.mask | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 230760b..b7e5303 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -32,6 +32,7 @@
 
 # Live ebuilds go here
 # keep this on top
+>=sci-libs/fftw-9999
 >=media-gfx/brlcad-9999
 >=dev-lang/path64-9999
 >=dev-lang/julia-9999

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

[Nicolas Bock]

commit:     ef511ece9cf6a8da286d81ffeb0b45c7f5984325
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Tue Sep 17 17:12:17 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Sep 17 17:12:17 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ef511ece

sci-chemistry/freeon: Added package masks to get an upgrade to version 1.0.

---
 profiles/package.mask | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index b7e5303..cc9f64d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -127,3 +127,11 @@ sci-visualization/vtkPOFFReader
 # Justin Lecher <jlec@gentoo.org> (11 May 2009)
 # work in progress 
 =sci-chemistry/almost-1.0.3-r1
+
+# Nicolas Bock <nicolasbock@gmail.com> (17 Sep 2003)
+# The versioning scheme of freeon changed from a date based version to a more
+# standard form. Now the latest release is considered a downgrade by portage.
+# Masking the date based releases to get users to upgrade.
+=sci-chemistry/freeon-2012.05.03
+=sci-chemistry/freeon-2013.09.12
+=sci-chemistry/freeon-2013.09.16

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

[Nicolas Bock]

commit:     98b6c227782c79342e17c6a7d230c4810704d1ca
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Thu Oct 24 18:00:40 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu Oct 24 18:00:40 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=98b6c227

sci-chemistry/freeon: Masking old version before removal.

---
 profiles/package.mask | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index cc9f64d..91d5c1e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -128,10 +128,17 @@ sci-visualization/vtkPOFFReader
 # work in progress 
 =sci-chemistry/almost-1.0.3-r1
 
-# Nicolas Bock <nicolasbock@gmail.com> (17 Sep 2003)
+# Nicolas Bock <nicolasbock@gmail.com> (17 Sep 2013)
 # The versioning scheme of freeon changed from a date based version to a more
 # standard form. Now the latest release is considered a downgrade by portage.
 # Masking the date based releases to get users to upgrade.
 =sci-chemistry/freeon-2012.05.03
 =sci-chemistry/freeon-2013.09.12
 =sci-chemistry/freeon-2013.09.16
+
+# Nicolas Bock <nicolasbock@gmail.com> (24 Oct 2013)
+# Masking older version before removal.
+=sci-chemistry/freeon-1.0
+=sci-chemistry/freeon-1.0.1
+=sci-chemistry/freeon-1.0.2
+=sci-chemistry/freeon-1.0.3

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

[Guillaume Horel]

commit:     baec37733adb335b6cb2c15180a165412a9d5f77
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Fri Oct 25 13:03:00 2013 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Mon Oct 28 04:17:28 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=baec3773

mask scilab-5.5.0 until release

---
 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 91d5c1e..306ba64 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -69,6 +69,13 @@
 >=sci-chemistry/coot-9999
 >=sci-chemistry/pymol-9999
 
+# Guillaume Horel <guillaume.horel@gmail.com> (25 Oct 2013)
+# mask new version of scilab until release
+>=sci-mathematics/scilab-5.5.0
+>=dev-java/jgraphx-2.1
+>=dev-java/jogl-2.0.2
+
+
 # Honza Macháček <Hloupy.Honza@centrum.cz> (17 June 2013)
 # bigdft moved from sci-libs to sci-physics
 # sci-physics/abinit now uses sci-libs/bigdft-abi instead

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

[Christoph Junghans]

commit:     c2f7deb3de021c95f2988362f162f3d0a1c43ddc
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Nov  5 23:43:38 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Nov  5 23:43:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c2f7deb3

masked dev-lang/conceptual[gui]

---
 profiles/package.use.mask | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 0bd0cfa..044007c 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -16,10 +16,10 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
-# Christoph Junghans <ottxor@gentoo.org> (27 Dec 2012)
-# icc/clang is not supported by all platforms
-dev-util/ccache icc clang
-
+# Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
+# gui sandbox error
+dev-lang/conceptual gui
+ 
 # Kacper Kowalik <xarthisius@gentoo.org> (23 Jul 2011)
 # mask assembler as it currently doesn't work
 dev-lang/path64 assembler

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

[Sebastien Fabbro]

commit:     32a7d816c71cd1c2131453772928d32037d853e7
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 26 21:06:26 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Nov 26 21:06:26 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=32a7d816

Masked live yt

---
 profiles/package.mask | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 306ba64..f99b182 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -64,6 +64,7 @@
 >=sci-chemistry/votca-csgapps-9999
 ~sci-visualization/gnuplot-4.6.9999
 ~sci-visualization/gnuplot-4.7.9999
+>=sci-visualization/yt-9999
 ~sci-chemistry/burrow-owl-9999_pre15
 >=sci-chemistry/pymol-apbs-plugin-9999
 >=sci-chemistry/coot-9999

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

[Nicolas Bock]

commit:     120bf63c24102acffbbbd22b704189b77b607b74
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Tue Dec 17 21:46:46 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Dec 17 21:47:20 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=120bf63c

Cleaning up masked sci-chemistry/freeon versions.

---
 profiles/package.mask | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 8f48c44..a86bd54 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -137,14 +137,6 @@ sci-visualization/vtkPOFFReader
 # work in progress 
 =sci-chemistry/almost-1.0.3-r1
 
-# Nicolas Bock <nicolasbock@gmail.com> (17 Sep 2013)
-# The versioning scheme of freeon changed from a date based version to a more
-# standard form. Now the latest release is considered a downgrade by portage.
-# Masking the date based releases to get users to upgrade.
-=sci-chemistry/freeon-2012.05.03
-=sci-chemistry/freeon-2013.09.12
-=sci-chemistry/freeon-2013.09.16
-
 # Nicolas Bock <nicolasbock@gmail.com> (24 Oct 2013)
 # Masking older version before removal.
 =sci-chemistry/freeon-1.0

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

[Nicolas Bock]

commit:     128eff2421168b83a710c1c63176c2b2cda438b0
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Tue Dec 17 21:49:11 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Dec 17 21:49:11 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=128eff24

Cleaning up package masks for removed sci-chemistry/freeon versions.

---
 profiles/package.mask | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index a86bd54..018cef9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -136,10 +136,3 @@ sci-visualization/vtkPOFFReader
 # Justin Lecher <jlec@gentoo.org> (11 May 2009)
 # work in progress 
 =sci-chemistry/almost-1.0.3-r1
-
-# Nicolas Bock <nicolasbock@gmail.com> (24 Oct 2013)
-# Masking older version before removal.
-=sci-chemistry/freeon-1.0
-=sci-chemistry/freeon-1.0.1
-=sci-chemistry/freeon-1.0.2
-=sci-chemistry/freeon-1.0.3

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

[Justin Lecher]

commit:     de62b1d46c8d6a45b8a4d4dc030a0352e99ec1d1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan  4 12:02:14 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan  4 12:02:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de62b1d4

mask sci-libs/dealii[metis] due to masked deps

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/package.use.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 044007c..95d7ff5 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -16,6 +16,10 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
+# Justin Lecher <jlec@gntoo.org> (04 Jan 2014)
+# sci-libs/parmetis-4* is masked
+sci-libs/dealii metis
+
 # Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
 # gui sandbox error
 dev-lang/conceptual gui

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

[Justin Lecher]

commit:     7b27e368300cffeb22c3f238fd58a8904cc20f50
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan  6 19:44:54 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  6 19:44:54 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7b27e368

Mask sci-biology/mne-python for missing dev-python/scikits-cuda

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/package.use.mask | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 95d7ff5..136fec3 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -16,7 +16,10 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
-# Justin Lecher <jlec@gntoo.org> (04 Jan 2014)
+# Justin Lecher <jlec@gntoo.org> (06 Jan 2014)
+# Missing dep dev-python/scikits-cuda
+sci-biology/mne-python cuda
+
 # sci-libs/parmetis-4* is masked
 sci-libs/dealii metis
 

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

[Reinis Danne]

commit:     399a67ee7e6c6bd1406ed3a8544190ae7245917f
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 21 17:03:57 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Tue Jan 21 17:03:57 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=399a67ee

masking live eselect

---
 profiles/package.mask | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 018cef9..79fd4af 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -32,6 +32,7 @@
 
 # Live ebuilds go here
 # keep this on top
+>=app-admin/eselect-9999
 >=sci-libs/fftw-9999
 >=media-gfx/brlcad-9999
 >=dev-lang/path64-9999

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

[Guillaume Horel]

commit:     23bce535ed3cd91a292ebae7bd8b26be622ef0fb
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Tue Apr 22 23:40:56 2014 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Tue Apr 22 23:46:37 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=23bce535

unmask scilab-5.5.0

---
 profiles/package.mask | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 6ab3cd1..f7c6aa4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,13 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Guillaume Horel <guillaume.horel@gmail.com> (25 Oct 2013)
-# mask new version of scilab until release
->=sci-mathematics/scilab-5.5.0
->=dev-java/jgraphx-2.1
->=dev-java/jogl-2.0.2
-
-
 # Honza Macháček <Hloupy.Honza@centrum.cz> (17 June 2013)
 # bigdft moved from sci-libs to sci-physics
 # sci-physics/abinit now uses sci-libs/bigdft-abi instead

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

[Jauhien Piatlicki]

commit:     940977f71da09710c17bdaa9fe7ad11b5afa9b11
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Tue Sep  9 13:31:59 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Tue Sep  9 13:31:59 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=940977f7

www-apps/py-swish-e: masked because of masked dependency

---
 profiles/ChangeLog    | 5 ++++-
 profiles/package.mask | 7 +++++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index 9759e42..0f103a6 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for profile directory
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  09 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> package.mask:
+  www-apps/py-swish-e: masked because of masked dependency
+
   09 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> package.mask:
   more sci-astronomy live ebuild masking
 

diff --git a/profiles/package.mask b/profiles/package.mask
index f7c6aa4..cb09f9e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,13 @@
 
 #--- END OF EXAMPLES ---
 
+# Jauhien Piatlicki <jauhien@gentoo.org> (09 Sep 2014)
+# www-apps/swish-e masked in tree for removal
+# www-apps/py-swish-e should be masked until
+# www-apps/swish-e is properly maintained and
+# reintroduced back in tree or science overlay
+www-apps/py-swish-e
+
 # Honza Macháček <Hloupy.Honza@centrum.cz> (17 June 2013)
 # bigdft moved from sci-libs to sci-physics
 # sci-physics/abinit now uses sci-libs/bigdft-abi instead

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

[Christoph Junghans]

commit:     65c3565eaed9ddade3c515a9c12e0d32eb14dedf
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 12 17:22:28 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Sep 12 17:22:28 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=65c3565e

added missing masks

---
 profiles/package.mask     | 10 ++++++++++
 profiles/package.use.mask |  4 ++++
 2 files changed, 14 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index cb09f9e..ca04efb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,16 @@
 
 #--- END OF EXAMPLES ---
 
+# Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
+# gcc:4.1 not available on no-multilib, selinux
+sci-chemistry/cpmgfit
+sci-chemistry/curvefit
+sci-chemistry/modelfree
+
+# Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
+# due to www-apps/py-swish-e being masked
+sci-chemistry/chimera-bin
+
 # Jauhien Piatlicki <jauhien@gentoo.org> (09 Sep 2014)
 # www-apps/swish-e masked in tree for removal
 # www-apps/py-swish-e should be masked until

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index d309713..f66f9b2 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -16,6 +16,10 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
+# Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
+# icc and ifc don't work on no-multilib
+sci-biology/estscan icc ifc
+
 # Justin Lecher <jlec@gntoo.org> (06 Jan 2014)
 # Missing dep dev-python/scikits-cuda
 sci-biology/mne-python cuda

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

[Jauhien Piatlicki]

commit:     24d9a8c1b6b9b3db2e959f41c6b0276a3e2e5d09
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 13 12:47:33 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sat Sep 13 12:47:33 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=24d9a8c1

mask dev-python/pythonocc because of bug #522678

---
 profiles/ChangeLog    | 3 +++
 profiles/package.mask | 6 ++++++
 2 files changed, 9 insertions(+)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index 0f103a6..4159567 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  13 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> package.mask:
+  mask dev-python/pythonocc because of bug #522678
+
   09 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> package.mask:
   www-apps/py-swish-e: masked because of masked dependency
 

diff --git a/profiles/package.mask b/profiles/package.mask
index ca04efb..601ecb6 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,12 @@
 
 #--- END OF EXAMPLES ---
 
+# Jauhien Piatlicki <jauhien@gentoo.org> (13 Sep 2014)
+# dev-python/pythonocc-0.5 works only with sci-libs/opencascade-6.3
+# which is not available in the tree, see bug #522678
+# mask until bug is not fixed
+dev-python/pythonocc
+
 # Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
 # gcc:4.1 not available on no-multilib, selinux
 sci-chemistry/cpmgfit

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

[Justin Lecher]

commit:     bf42c35247e392e05de74c975cd39353c1b703da
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 15 06:31:58 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 15 06:31:58 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bf42c352

Drop obsolete masks

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/ChangeLog    | 3 +++
 profiles/package.mask | 4 ----
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index 4159567..feeac1b 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Sep 2014; Justin Lecher <jlec@gentoo.org> package.mask:
+  Drop obsolete masks
+
   13 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> package.mask:
   mask dev-python/pythonocc because of bug #522678
 

diff --git a/profiles/package.mask b/profiles/package.mask
index 601ecb6..4381d71 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -42,10 +42,6 @@ sci-chemistry/cpmgfit
 sci-chemistry/curvefit
 sci-chemistry/modelfree
 
-# Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
-# due to www-apps/py-swish-e being masked
-sci-chemistry/chimera-bin
-
 # Jauhien Piatlicki <jauhien@gentoo.org> (09 Sep 2014)
 # www-apps/swish-e masked in tree for removal
 # www-apps/py-swish-e should be masked until

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

[Justin Lecher]

commit:     522087642179eb2e08d933d07364351ee8f5fb7d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 13:15:42 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 13:15:42 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=52208764

Unmask false global masks

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/ChangeLog    | 3 +++
 profiles/package.mask | 6 ------
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index feeac1b..a954117 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Sep 2014; Justin Lecher <jlec@gentoo.org> package.mask:
+  Unmask false global masks
+
   15 Sep 2014; Justin Lecher <jlec@gentoo.org> package.mask:
   Drop obsolete masks
 

diff --git a/profiles/package.mask b/profiles/package.mask
index 4381d71..c4a8902 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -36,12 +36,6 @@
 # mask until bug is not fixed
 dev-python/pythonocc
 
-# Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
-# gcc:4.1 not available on no-multilib, selinux
-sci-chemistry/cpmgfit
-sci-chemistry/curvefit
-sci-chemistry/modelfree
-
 # Jauhien Piatlicki <jauhien@gentoo.org> (09 Sep 2014)
 # www-apps/swish-e masked in tree for removal
 # www-apps/py-swish-e should be masked until

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

[Andreas Hüttel]

commit:     dc1007b12fceb95eeb4f090cff3f225ff0e36b27
Author:     Andreas K. Huettel (dilfridge) <dilfridge <AT> gentoo <DOT> org>
AuthorDate: Sat Nov  1 17:19:20 2014 +0000
Commit:     Andreas Hüttel <dilfridge <AT> gentoo <DOT> org>
CommitDate: Sat Nov  1 17:19:20 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dc1007b1

Mask Lab::Instrument and Lab::Tools for removal

---
 profiles/ChangeLog    | 3 +++
 profiles/package.mask | 8 ++++++++
 2 files changed, 11 insertions(+)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index a954117..10d6ec5 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  01 Nov 2014; Andreas K. Huettel <dilfridge@gentoo.org> package.mask:
+  Mask Lab::Instrument and Lab::Tools for removal
+
   16 Sep 2014; Justin Lecher <jlec@gentoo.org> package.mask:
   Unmask false global masks
 

diff --git a/profiles/package.mask b/profiles/package.mask
index c4a8902..b831700 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,14 @@
 
 #--- END OF EXAMPLES ---
 
+# Andreas K. Huettel <dilfridge@gentoo.org> (1 Nov 2014)
+# Lab::Instrument and Lab::Tools provided as separate packages
+# are way outdated. These are now supplied as parts of the package
+# Lab::Measurement (dev-perl/Lab-Measurement in the main portage
+# tree). Masked for removal.
+dev-perl/Lab-Instrument
+dev-perl/Lab-Tools
+
 # Jauhien Piatlicki <jauhien@gentoo.org> (13 Sep 2014)
 # dev-python/pythonocc-0.5 works only with sci-libs/opencascade-6.3
 # which is not available in the tree, see bug #522678

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

[Christoph Junghans]

commit:     c7967190beccd959c121a688463ee692fde459a8
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 15 00:59:05 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Nov 15 00:59:05 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c7967190

sci-misc/salome-* masked for removal

---
 profiles/package.mask | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index b831700..69e1676 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,21 @@
 
 #--- END OF EXAMPLES ---
 
+# Christoph Junghans <ottxor@gentoo.org> (14 Nov 2014)
+# sci-misc/salome-* masked for removal in 30 days
+# not bumped since 2010, reintroduced back in science overlay
+# if properly maintained
+sci-misc/salome-component
+sci-misc/salome-geom
+sci-misc/salome-gui
+sci-misc/salome-kernel
+sci-misc/salome-med
+sci-misc/salome-meta
+sci-misc/salome-pycalculator
+sci-misc/salome-smesh
+sci-misc/salome-visu
+sci-misc/salome-yacs
+
 # Andreas K. Huettel <dilfridge@gentoo.org> (1 Nov 2014)
 # Lab::Instrument and Lab::Tools provided as separate packages
 # are way outdated. These are now supplied as parts of the package

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

[Christoph Junghans]

commit:     e2f5b67f08425a27ac5808f3381f2e93cd8041e3
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 24 21:41:21 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Nov 24 21:41:21 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e2f5b67f

drop www-apps/py-swish-e mask

---
 profiles/ChangeLog    | 3 +++
 profiles/package.mask | 7 -------
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/profiles/ChangeLog b/profiles/ChangeLog
index 10d6ec5..4566ad8 100644
--- a/profiles/ChangeLog
+++ b/profiles/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  24 Nov 2014; Christoph Junghans <ottxor@gentoo.org> package.mask:
+  drop www-apps/py-swish-e mask
+
   01 Nov 2014; Andreas K. Huettel <dilfridge@gentoo.org> package.mask:
   Mask Lab::Instrument and Lab::Tools for removal
 

diff --git a/profiles/package.mask b/profiles/package.mask
index 69e1676..defec5b 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -59,13 +59,6 @@ dev-perl/Lab-Tools
 # mask until bug is not fixed
 dev-python/pythonocc
 
-# Jauhien Piatlicki <jauhien@gentoo.org> (09 Sep 2014)
-# www-apps/swish-e masked in tree for removal
-# www-apps/py-swish-e should be masked until
-# www-apps/swish-e is properly maintained and
-# reintroduced back in tree or science overlay
-www-apps/py-swish-e
-
 # Honza Macháček <Hloupy.Honza@centrum.cz> (17 June 2013)
 # bigdft moved from sci-libs to sci-physics
 # sci-physics/abinit now uses sci-libs/bigdft-abi instead

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

[Christoph Junghans]

commit:     3b85486eea5913d11359a975abffe1bd6a175c42
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Mon Jan 26 09:47:17 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 26 10:09:52 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3b85486e

Add profiles/license_groups

---
 profiles/license_groups | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/license_groups b/profiles/license_groups
new file mode 100644
index 0000000..d8f74d9
--- /dev/null
+++ b/profiles/license_groups
@@ -0,0 +1 @@
+EULA NVIDIA-gdk

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

[Justin Lecher]

commit:     09cd4000c1f78950a85cfdbd8c10cfd637fdd6ff
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb  4 08:53:52 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb  4 08:53:52 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=09cd4000

Drop obsolete maskes

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/package.mask | 24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 01dacb7..d97a441 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -81,30 +81,6 @@ sci-biology/artemis-bin
 # masked until reverse depedencies are fixed
 >=sci-libs/parmetis-4
 
-# Justin Lecher <jlec@gentoo.org> (20 Feb 2012)
-# They are broken in one or the other way
-# Need to be bumped to emboss-6.4.0
-<sci-biology/emboss-6.6.0
-<sci-biology/embassy-6.6.0
-<sci-biology/embassy-cbstools-1.0.0.650
-<sci-biology/embassy-clustalomega-1.1.0
-<sci-biology/embassy-domainatrix-0.1.650
-<sci-biology/embassy-domalign-0.1.650
-<sci-biology/embassy-domsearch-0.1.650
-<sci-biology/embassy-emnu-1.05.650
-<sci-biology/embassy-esim4-1.0.0.650
-<sci-biology/embassy-hmmer-2.3.2.650
-<sci-biology/embassy-iprscan-4.3.1.650
-<sci-biology/embassy-meme-4.7.650
-sci-biology/embassy-memenew
-sci-biology/embassy-mira
-<sci-biology/embassy-mse-3.0.0.650
-<sci-biology/embassy-phylipnew-3.69.650
-<sci-biology/embassy-signature-0.1.650
-<sci-biology/embassy-structure-0.1.650
-<sci-biology/embassy-topo-2.0.650
-<sci-biology/embassy-vienna-1.7.2.650
-
 # Justin Lecher <jlec@gentoo.org> (24 Jun 2011)
 # paraview dep is masked
 sci-visualization/vtkPOFFReader

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

[Justin Lecher]

commit:     ecdf49fb515a8ef813b7d43ca05cda440d4dbceb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Feb  5 20:28:10 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 11 09:12:47 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecdf49fb

Import categories

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/categories | 127 +++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 126 insertions(+), 1 deletion(-)

diff --git a/profiles/categories b/profiles/categories
index e1fb024..feb3006 100644
--- a/profiles/categories
+++ b/profiles/categories
@@ -1,27 +1,124 @@
+app-accessibility
 app-admin
+app-antivirus
+app-arch
+app-backup
 app-benchmarks
+app-cdr
+app-crypt
+app-dicts
 app-doc
+app-editors
+app-emacs
+app-emulation
+app-forensics
+app-i18n
+app-laptop
+app-leechcraft
+app-misc
+app-mobilephone
+app-office
+app-officeext
+app-pda
 app-portage
+app-shells
 app-text
 app-vim
+app-xemacs
+dev-ada
 dev-cpp
+dev-db
+dev-dotnet
+dev-embedded
+dev-games
+dev-haskell
 dev-java
 dev-lang
 dev-libs
+dev-lisp
+dev-lua
 dev-ml
 dev-perl
+dev-php
 dev-python
+dev-qt
+dev-ruby
+dev-scheme
 dev-tcltk
 dev-tex
+dev-texlive
 dev-util
+dev-vcs
+games-action
+games-arcade
+games-board
+games-emulation
+games-engines
+games-fps
+games-kids
+games-misc
+games-mud
+games-puzzle
+games-roguelike
+games-rpg
+games-server
+games-simulation
+games-sports
+games-strategy
+games-util
+gnome-base
+gnome-extra
+gnustep-apps
+gnustep-base
+gnustep-libs
+gpe-base
+gpe-utils
+java-virtuals
+kde-base
+kde-frameworks
+kde-misc
+kde-plasma
+lxde-base
+lxqt-base
+mail-client
+mail-filter
+mail-mta
+mate-base
+mate-extra
+media-fonts
 media-gfx
 media-libs
+media-plugins
+media-radio
+media-sound
+media-tv
+media-video
+net-analyzer
+net-dialup
+net-dns
 net-firewall
+net-fs
 net-ftp
+net-im
+net-irc
+net-libs
+net-mail
 net-misc
+net-nds
+net-news
+net-nntp
+net-p2p
+net-print
+net-proxy
+net-voip
+net-wireless
+net-zope
 perl-core
+rox-base
+rox-extra
 sci-astronomy
 sci-biology
+sci-calculators
 sci-chemistry
 sci-electronics
 sci-geosciences
@@ -30,9 +127,37 @@ sci-mathematics
 sci-misc
 sci-physics
 sci-visualization
+sec-policy
+sys-apps
+sys-auth
+sys-block
+sys-boot
 sys-cluster
 sys-devel
+sys-firmware
+sys-freebsd
 sys-fs
-virtual
+sys-infiniband
+sys-kernel
+sys-libs
+sys-power
+sys-process
+www-apache
 www-apps
+www-client
+www-misc
+www-plugins
+www-servers
+x11-apps
+x11-base
+x11-drivers
 x11-libs
+x11-misc
+x11-plugins
+x11-proto
+x11-terms
+x11-themes
+x11-wm
+xfce-base
+xfce-extra
+virtual

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

[Justin Lecher]

commit:     0f4b2a84b33a706836003d2a8f21d6d55ac8a8b6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 09:08:55 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 09:08:55 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0f4b2a84

Update CATs

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/categories | 123 ++--------------------------------------------------
 1 file changed, 3 insertions(+), 120 deletions(-)

diff --git a/profiles/categories b/profiles/categories
index feb3006..2060a47 100644
--- a/profiles/categories
+++ b/profiles/categories
@@ -1,124 +1,33 @@
-app-accessibility
 app-admin
-app-antivirus
-app-arch
-app-backup
 app-benchmarks
-app-cdr
-app-crypt
-app-dicts
 app-doc
 app-editors
-app-emacs
-app-emulation
 app-forensics
-app-i18n
-app-laptop
-app-leechcraft
-app-misc
-app-mobilephone
-app-office
-app-officeext
-app-pda
 app-portage
-app-shells
 app-text
 app-vim
-app-xemacs
-dev-ada
 dev-cpp
-dev-db
-dev-dotnet
-dev-embedded
-dev-games
-dev-haskell
 dev-java
 dev-lang
 dev-libs
-dev-lisp
 dev-lua
 dev-ml
 dev-perl
-dev-php
 dev-python
-dev-qt
-dev-ruby
-dev-scheme
 dev-tcltk
 dev-tex
-dev-texlive
 dev-util
-dev-vcs
-games-action
-games-arcade
-games-board
-games-emulation
-games-engines
-games-fps
-games-kids
-games-misc
-games-mud
-games-puzzle
-games-roguelike
-games-rpg
-games-server
-games-simulation
-games-sports
-games-strategy
-games-util
-gnome-base
-gnome-extra
-gnustep-apps
-gnustep-base
-gnustep-libs
-gpe-base
-gpe-utils
-java-virtuals
-kde-base
-kde-frameworks
-kde-misc
-kde-plasma
-lxde-base
-lxqt-base
-mail-client
-mail-filter
-mail-mta
-mate-base
-mate-extra
-media-fonts
 media-gfx
 media-libs
-media-plugins
-media-radio
-media-sound
-media-tv
-media-video
-net-analyzer
-net-dialup
-net-dns
+metadata
 net-firewall
-net-fs
 net-ftp
-net-im
-net-irc
 net-libs
-net-mail
 net-misc
-net-nds
-net-news
-net-nntp
-net-p2p
-net-print
-net-proxy
-net-voip
-net-wireless
-net-zope
+patches
 perl-core
-rox-base
-rox-extra
 sci-astronomy
 sci-biology
-sci-calculators
 sci-chemistry
 sci-electronics
 sci-geosciences
@@ -127,37 +36,11 @@ sci-mathematics
 sci-misc
 sci-physics
 sci-visualization
-sec-policy
 sys-apps
-sys-auth
-sys-block
-sys-boot
 sys-cluster
 sys-devel
-sys-firmware
-sys-freebsd
-sys-fs
 sys-infiniband
-sys-kernel
-sys-libs
-sys-power
 sys-process
-www-apache
-www-apps
-www-client
-www-misc
-www-plugins
-www-servers
-x11-apps
-x11-base
-x11-drivers
+virtual
 x11-libs
 x11-misc
-x11-plugins
-x11-proto
-x11-terms
-x11-themes
-x11-wm
-xfce-base
-xfce-extra
-virtual

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

[Justin Lecher]

commit:     de6b31f68d1f356fe8115fc35b71d180ed8ff5b2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 09:39:21 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 09:39:21 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de6b31f6

Clean CATS some more

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 profiles/categories | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/categories b/profiles/categories
index 2060a47..609bef2 100644
--- a/profiles/categories
+++ b/profiles/categories
@@ -19,12 +19,10 @@ dev-tex
 dev-util
 media-gfx
 media-libs
-metadata
 net-firewall
 net-ftp
 net-libs
 net-misc
-patches
 perl-core
 sci-astronomy
 sci-biology

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

[Andrew Savchenko]

commit:     e4112f7c9697b60e505c1c4dd04affe3e07cae3f
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Sat Feb 28 04:47:02 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
CommitDate: Sat Feb 28 04:47:02 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e4112f7c

profiles/categories cleanup: remove stray sys-process category

---
 profiles/categories | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/categories b/profiles/categories
index 95d6dab..34c941a 100644
--- a/profiles/categories
+++ b/profiles/categories
@@ -37,7 +37,6 @@ sys-apps
 sys-cluster
 sys-devel
 sys-infiniband
-sys-process
 virtual
 x11-libs
 x11-misc

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

[Justin Lecher]

commit:     33ff3ca2d8a5c7c4499aa75481aa57453f3ef42c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun  3 10:21:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun  3 10:21:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=33ff3ca2

Clean CATs

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/categories | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/profiles/categories b/profiles/categories
index 34c941a..20ed0d6 100644
--- a/profiles/categories
+++ b/profiles/categories
@@ -1,7 +1,6 @@
 app-admin
 app-benchmarks
 app-doc
-app-editors
 app-forensics
 app-portage
 app-text
@@ -10,7 +9,6 @@ dev-cpp
 dev-java
 dev-lang
 dev-libs
-dev-lua
 dev-ml
 dev-perl
 dev-python
@@ -33,7 +31,6 @@ sci-mathematics
 sci-misc
 sci-physics
 sci-visualization
-sys-apps
 sys-cluster
 sys-devel
 sys-infiniband

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

[Justin Lecher]

commit:     4fc6905a6afd491dbc046bde99c2a65c21df606b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Sep  4 09:27:36 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep  4 09:27:47 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4fc6905a

Update USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 387 +++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 301 insertions(+), 86 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 3193225..855f59c 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -2,82 +2,193 @@
 # your descriptions to your package's metadata.xml ONLY.
 # * generated automatically using egencache *
 
-dev-cpp/eigen:adolc - Enable use for automatic differentiation using sci-libs/adolc
+app-doc/root-docs:api - Generate html API documentation
+app-doc/root-docs:http - Build HttpServer documentation
+app-doc/root-docs:math - Provide all math related documentation
+app-doc/root-docs:metric - Default to A4 paper size and metric measurement. Letter will be used otherwise
+dev-cpp/eigen:adolc - Enable automatic differentiation using sci-libs/adolc
+dev-cpp/eigen:metis - Enable matrix partitioning using sci-libs/metis
+dev-cpp/eigen:mkl - Use propertary intel blas/lapack implementation through sci-libs/mkl
+dev-cpp/eigen:pastix - Enable large scale direct solver with using sci-libs/pastix
 dev-cpp/eigen:sparse - Enable use for extra sparse matrix with sci-libs/umfpack, sci-libs/cholmod, sci-libs/superlu and dev-cpp/sparsehash
 dev-java/hdf-java:hdf - Add support for the Hierarchical Data Format v.4 (sci-libs/hdf)
 dev-java/hdf-java:hdfview - Build a GUI viewer for all files supported in dev-java/hdf-java
 dev-java/jogl:cg - Enable NVidia Cg binding.
-dev-lang/icc:eclipse - Install the dev-util/eclipse-sdk plugins
-dev-lang/idb:eclipse - Install the dev-util/eclipse-sdk plugins
+dev-lang/berkeley_upc:mpi-compat - Enable interoperability with MPI
+dev-lang/berkeley_upc:pshm - Build UPC Runtime/GASNet with Process-SHared Memory enabled
+dev-lang/berkeley_upc:segment-fast - Select GASNet's FAST segments (default), for the fastest remote access with a possible cost in max shared memory size
+dev-lang/berkeley_upc:segment-large - Select GASNet's LARGE segments, for the largest possible shared memory size, at a possible cost in remote access time
+dev-lang/berkeley_upc:single - Support running over smp loopback (no network)
+dev-lang/berkeley_upc:sptr-packed - Use the more efficient 'packed' shared pointer representation
+dev-lang/berkeley_upc:sptr-struct - Use the 'struct' shared pointer representation
+dev-lang/berkeley_upc:sptr-symmetric - Enable 'symmetric' pointer variant where available (64-bit smp and shmem)
+dev-lang/berkeley_upc:udp - Support running over UDP
+dev-lang/conceptual:gui - Build the Java base graphical interface
+dev-lang/julia:int64 - Build with 64 bits integer blas and lapack (needs sci-libs/openblas and sci-libs/lapack-reference)
 dev-lang/path64:assembler - Build PathAS assembler
 dev-lang/path64:debugger - Build PathDB debugger
 dev-lang/path64:native - Use EKOPath/Path64 for bootstraping
 dev-lang/path64:valgrind - Support compiler debugging with dev-util/valgrind
-dev-libs/intel-common:compiler - Install the libraries needed for the icc and ifort compilers
-dev-ml/mlgmpidl:mpfr - add support for mpfr, the library for multiple-precision floating-point computations with exact rounding
-dev-ml/zarith:mpir - Use mpir library instead of gmp
+dev-lang/pgi:acml - Install AMD's core math library.
+dev-lang/pgi:cuda - Install PGI's CUDA components (e.g. for OpenACC)
+dev-lang/pgi:java - Install a PGI-tuned JRE.
+dev-libs/boost:context - Build and install the Boost.Context library and all other Boostlibraries that depends on it
+dev-libs/boost:debug - Build and install only the debug version of the Boost libraries. Only enable this flag if you're developing against boost.
+dev-libs/boost:doc - Install the full API documentation documentation. This takes over 200MB of extra disk space.
+dev-libs/boost:nls - Build libboost_locale. This library requires compatible C library interfaces, which might not be provided by uClibc or other embedded libraries.
+dev-libs/boost:threads - Build multi-thread-compatible libraries instead of single-threaded only.
+dev-libs/boost:tools - Build and install the boost tools (bcp, quickbook, inspect, wave)
+dev-libs/libflatarray:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator)
+dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
+dev-ml/zarith:mpir - Use sci-libs/mpir for arbitrary precision integer arithmetic
 dev-python/ffnet:matplotlib - Use matplotlib for drawing
+dev-python/ipython:matplotlib - Add support for dev-python/matplotlib
+dev-python/ipython:mongodb - Enable support for MongoDB via dev-python/pymongo
+dev-python/ipython:nbconvert - Enable support for converting notebooks to various formats using app-text/pandoc
+dev-python/ipython:notebook - Install requirements for the web notebook based on www-servers/tornado
 dev-python/pyhdf:szip - Allow to use sci-libs/szip for SZIP compression method in SDsetcompress()
-dev-util/nvidia-cuda-sdk:cuda - Build CUDA binaries
-dev-util/nvidia-cuda-sdk:opencl - Build OpenCL binaries
-dev-util/nvidia-cuda-toolkit:debugger - Installs the NVIDIA CUDA debugger
-dev-util/nvidia-cuda-toolkit:profiler - Installs the NVIDIA CUDA visual profiler
+dev-python/ufl:scipy - Adds support for evaluating Bessel functions using dev-python/scipy
+dev-tex/pythontex:highlighting - PLEASE FIX MY DESCRIPTION
+dev-util/VampirTrace:cuda - Enable tracing of CUDA calls and GPU kernels.
+dev-util/amdapp:examples - Build the OpenCL example programs
+dev-util/nvidia-cuda-gdk:healthmon - Install nvidia-healthmon.
+dev-util/nvidia-cuda-gdk:nvml - Install the NVIDIA Managment Library.
+dev-util/nvidia-cuda-gdk:nvvs - Install the NVIDIA Validation Suite.
+dev-util/nvidia-cuda-sdk:cuda - Build CUDA binaries.
+dev-util/nvidia-cuda-sdk:opencl - Build OpenCL binaries.
+dev-util/nvidia-cuda-toolkit:debugger - Installs the CUDA debugger.
+dev-util/nvidia-cuda-toolkit:eclipse - Install the dev-util/eclipse-sdk plugins
+dev-util/nvidia-cuda-toolkit:profiler - Installs the NVIDIA CUDA visual profiler.
 media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled)
-net-fs/cvmfs:client - Install the cvmfs client programs and init script
-net-fs/cvmfs:server - Install the cvmfsd program and init script
-net-misc/dhcp:client - Install the dhclient program
-net-misc/dhcp:server - Install the dhcpd and dhcrelay programs
+media-gfx/librecad:3d - Require all 2D coordinates stored as 3D
+media-gfx/librecad:tools - Build additional tool programs: tff2lff
+sci-astronomy/astrometry:extra - Add extra tools, specifically for plots
+sci-astronomy/mosstack:opencl - Enables OpenCL support and pulls in pyopencl. This makes some operations much faster but requires specific hardware and drivers.
+sci-astronomy/mosstack:qt4 - Pulls in PyQt4. Program works on command line interface without it but for GUI the library is required.
 sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
 sci-astronomy/scamp:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
 sci-astronomy/sextractor:modelfit - Enable profile model fitting, needs sci-libs/atlas and sci-libs/fftw
 sci-astronomy/zpeg:gdl - Install GDL/IDL plotting routines
-sci-chemistry/avogadro:glsl - Enable glsl features via GLEW.
+sci-biology/discrover:cairo - Use Cairo for sequence logo plotting capabilities
+sci-biology/discrover:dreme - Enable usage of DREME from the MEME package for seeding
+sci-biology/discrover:lto - Compile with link-time optimization (LTO)
+sci-biology/discrover:misc_scripts - Install miscellaneous scripts
+sci-biology/discrover:rmathlib - Link to the standalone Rmathlib for statistical routines
+sci-biology/estscan:icc - Undocumented USE
+sci-biology/estscan:ifc - Undocumented USE
+sci-biology/exonerate-gff3:utils - Unknown
+sci-biology/ncbi-blast+:boost - Undocumented USE
+sci-biology/ncbi-blast+:cppunit - Undocumented USE
+sci-biology/ncbi-blast+:freetype - Undocumented USE
+sci-biology/ncbi-blast+:mesa - Undocumented USE
+sci-biology/ncbi-blast+:muparser - Undocumented USE
+sci-biology/ncbi-blast+:sablotron - Undocumented USE
+sci-biology/ncbi-blast+:sqlite3 - Add support for dev-db/sqlite:3
+sci-biology/ncbi-blast+:xalan - Undocumented USE
+sci-biology/ncbi-blast+:xerces - Undocumented USE
+sci-biology/ncbi-blast+:xslt - Undocumented USE
+sci-biology/ncbi-tools++:boost - Undocumented USE
+sci-biology/ncbi-tools++:cppunit - Undocumented USE
+sci-biology/ncbi-tools++:freetype - Undocumented USE
+sci-biology/ncbi-tools++:mesa - Undocumented USE
+sci-biology/ncbi-tools++:muparser - Undocumented USE
+sci-biology/ncbi-tools++:sablotron - Undocumented USE
+sci-biology/ncbi-tools++:sqlite3 - Add support for dev-db/sqlite:3
+sci-biology/ncbi-tools++:xalan - Undocumented USE
+sci-biology/ncbi-tools++:xerces - Undocumented USE
+sci-biology/ncbi-tools++:xslt - Undocumented USE
+sci-biology/sga:jemalloc - Use dev-libs/jemalloc
+sci-biology/tophat:bam - Compile support for the BAM format
+sci-chemistry/avogadro2:rpc - Enable RPC server
 sci-chemistry/ball:cuda - Include cuda support
 sci-chemistry/ball:sql - Include SQL database support
-sci-chemistry/ball:webkit - Uses x11-libs/qt-webkit for drawing
-sci-chemistry/gromacs:avx128fma - Enable 128bit avx with fma (e.g. AMD BullDozer)
-sci-chemistry/gromacs:avx256 - Enable 256bit avx (e.g. Intel Sandy Bridge)
+sci-chemistry/ball:webkit - Uses dev-qt/qt-webkit for drawing
+sci-chemistry/gamess:neo - Enable NEO for nuclear basis support
+sci-chemistry/gamess:pax_kernel - Make this package work on PAX kernels
+sci-chemistry/gamess:qmmm-tinker - Enable tinker qmmm code
+sci-chemistry/gnome-chemistry-utils:gnumeric - Build pluging for gnumeric
+sci-chemistry/gromacs:boost - Enable external boost library
 sci-chemistry/gromacs:cuda - Enable cuda non-bonded kernels
 sci-chemistry/gromacs:double-precision - More precise calculations at the expense of speed
-sci-chemistry/gromacs:fkernels - Enable building of Fortran Kernels for platforms that dont have assembly loops
-sci-chemistry/gromacs:hybrid - Enable hybrid acceleration kernels
-sci-chemistry/gromacs:power6 - Enable Power6 optimizations
+sci-chemistry/gromacs:make-symlinks - Create symbolic links for pre-5.0 binary names
+sci-chemistry/gromacs:mkl - Use sci-libs/mkl for fft, blas, lapack routines
+sci-chemistry/gromacs:offensive - Enable gromacs partly offensive quotes
 sci-chemistry/gromacs:single-precision - Single precision version of gromacs (default)
-sci-chemistry/gromacs:sse41 - Enable sse4.1 acceleration
-sci-chemistry/jmol:client-only - Install the viewer only, no applet files for httpd
+sci-chemistry/gromacs:tng - Enable new trajectory format - tng
+sci-chemistry/mdsctk:R - Install dev-lang/R scripts as well
+sci-chemistry/nwchem:blas - Use external BLAS library instead of the internal routines
+sci-chemistry/nwchem:cuda - Enable CUDA GPU support for the Tensor Contraction Engine generated methods (CI, MBPT, CC)
+sci-chemistry/nwchem:int64 - Use 64 bits integers
+sci-chemistry/nwchem:lapack - Use external LAPACK library instead of the internal routines
+sci-chemistry/nwchem:mrcc - Compile the routines for Multi Reference Coupled Clusters theory
+sci-chemistry/nwchem:nwchem-tests - Install qa tests data
+sci-chemistry/nwchem:scalapack - Use external SCALAPACK library
+sci-chemistry/openbabel:doc - Install API dicumentation.
+sci-chemistry/openbabel:java - Install Java bindings.
+sci-chemistry/openbabel:openmp - Enable parallelization using OpenMP.
+sci-chemistry/openbabel:perl - Install Perl bindings.
+sci-chemistry/openbabel:python - Install Python bindings and PyBel.
+sci-chemistry/openbabel:ruby - Install Ruby bindings.
+sci-chemistry/openbabel:wxwidgets - Build Open Babel GUI.
 sci-chemistry/pymol:apbs - Pymol supprt for sci-chemistry/apbs
-sci-chemistry/pymol:numpy - Enable numpy support for Pymol
-sci-chemistry/pymol:vmd - Builds molfile plugin support
 sci-chemistry/pymol:web - Install Pymodule needed for web app support
 sci-chemistry/rosetta:boinc - compile rosetta as a rosetta@home client
 sci-chemistry/rosetta:boost - compile rosetta with boost supported code
+sci-chemistry/rosetta:float - Build with floats rather than doubles
+sci-chemistry/rosetta:lange - Apply patches from www.csrosetta.org
+sci-chemistry/shiftx2:debug - Enables debug output in the shiftx2 java part
 sci-chemistry/votca-csg:extras - Pull in extra applications from sci-chemistry/votca-csg-apps
 sci-chemistry/votca-csg:gromacs - Add support for gromacs file formats through sci-chemistry/gromacs
 sci-electronics/player:boost - Automatically generated description for boost
 sci-electronics/player:festival - Automatically generated description for festival
 sci-electronics/player:openssl - Automatically generated description for openssl
 sci-electronics/player:sphinx2 - Automatically generated description for sphinx2
-sci-geosciences/libtcd:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only.
 sci-geosciences/qgis:grass - Add support for sci-geosciences/grass
-sci-geosciences/xtide:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only.
 sci-libs/acml:gfortran - Fetch and install acml compiled with GNU FORTRAN compiler
 sci-libs/acml:ifort - Fetch and install acml compiled with the Intel FORTRAN compiler
 sci-libs/acml:int64 - Install the 64 bits integer library
-sci-libs/acml:nag - Fetch and install acml compiled with the NAG FORTRAN compiler
 sci-libs/acml:open64 - Fetch and install acml compiled with the Open64 FORTRAN Compiler
 sci-libs/acml:pgi - Fetch and install acml compiled with the Portland Group FORTRAN compiler
-sci-libs/armadillo:atlas - Link with ATLAS libraries for cblas and clapack (needs sci-libs/lapack-atlas)
+sci-libs/armadillo:arpack - Link with sci-libs/arpack libraries for eigen decomposition
+sci-libs/armadillo:atlas - Link with sci-libs/atlas libraries for cblas and clapack
+sci-libs/armadillo:mkl - Use matrix allocation from the Intel MKL sci-libs/mkl
+sci-libs/armadillo:superlu - Use SuperLU for sparse linear equation solving sci-libs/superlu
+sci-libs/armadillo:tbb - Use matrix allocation from the Threads Building Blocks dev-cpp/tbb
+sci-libs/arrayfire:cpu - Enable CPU Build.
+sci-libs/arrayfire:cuda - Enable CUDA Build.
+sci-libs/arrayfire:opencl - Enable OpenCL Build.
+sci-libs/asl:matio - Matlab support with sci-libs/matio
 sci-libs/atlas:generic - Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)
-sci-libs/bigdft:cuda - Add cuda support
+sci-libs/bigdft-abi:cuda - Enable support for nVidia CUDA
+sci-libs/bigdft-abi:etsf_io - Enable support for reading and writing the European Theoretical Spectroscopy facility (ETSF) file format
+sci-libs/bigdft-abi:glib - Compile with GLib Object System support
+sci-libs/bigdft-abi:opencl - Enable support for OpenCL GPU acceleration
+sci-libs/bigdft-abi:scalapack - Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing
+sci-libs/blas-reference:int64 - Build the 64 bits integer library
 sci-libs/calculix-ccx:arpack - Add sparse eigen value support via sci-libs/arpack
-sci-libs/coinor-clp:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
-sci-libs/coinor-clp:metis - Enable partitioning with sci-libs/metis
-sci-libs/coinor-clp:mumps - Enable sci-libs/mumps support
-sci-libs/coinor-clp:sparse - Enable support for sparse matrix with sci-libs/cholmod
-sci-libs/coinor-osi:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
-sci-libs/coinor-symphony:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
-sci-libs/coinor-utils:glpk - Enable GNU Linear Programming Kit sci-mathematics/glpk support
+sci-libs/cblas-reference:int64 - Build the 64 bits integer library
+sci-libs/clblas:client - Build a command line clBLAS client program.
+sci-libs/clblas:ktest - A command line tool for testing single clBLAS kernel.
+sci-libs/clblas:performance - Copy performance scripts that can measure and graph performance.
+sci-libs/clrng:client - Build a command line clRNG client program.
+sci-libs/dealii:arpack - Adds support for ARPACK (sci-libs/arpack)
+sci-libs/dealii:c++11 - Compile the library with -std=c++11
+sci-libs/dealii:debug - Build an additional debug library with extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see <http://www.gentoo.org/proj/en/qa/backtraces.xml>
+sci-libs/dealii:mesh_converter - Build and install the mesh_converter executable
+sci-libs/dealii:metis - Add support for metis (sci-libs/metis)
+sci-libs/dealii:mumps - Add support for mumps (sci-libs/mumps)
+sci-libs/dealii:muparser - Add support for muparser (dev-cpp/muParser)
+sci-libs/dealii:opencascade - Add support for opencascade (sci-libs/opencascade)
+sci-libs/dealii:p4est - Add support for p4est (sci-mathematics/p4est)
+sci-libs/dealii:parameter_gui - Build and install the parameter_gui executable
+sci-libs/dealii:petsc - Add support for petsc (sci-libs/petsc)
+sci-libs/dealii:sparse - Add support for suitesparse (sci-libs/suitesparse)
+sci-libs/dealii:tbb - Add threading support with the help of the tbb library (dev-cpp/tbb)
+sci-libs/dealii:trilinos - Add support for trilinos (sci-libs/trilinos)
+sci-libs/etsf_io:pic - Compile Position Independent Code
 sci-libs/factory:singular - Enable support for sci-mathematics/singular
+sci-libs/fftw:quad - Build quadruple precision lib
+sci-libs/fftw:zbus - Adds support for ZBus cycle-counter of mips
 sci-libs/fox:dom - Compile the W3C document object model module
 sci-libs/fox:fast - Compile with best known optimization flags
 sci-libs/fox:sax - Compile the streaming, validating parser based on java's Simple API for XML
@@ -96,62 +207,117 @@ sci-libs/gmsh:tetgen - Enable 3D delauny triangulation using tetgen lib
 sci-libs/gotoblas2:dynamic - Build dynamic architecture detection at run time (for multi targets)
 sci-libs/gotoblas2:incblas - Build the CBLAS interface
 sci-libs/gotoblas2:int64 - Build the 64 bits integer library
-sci-libs/ipopt:mumps - Enable sci-libs/mumps support
+sci-libs/gsl:cblas-external - Link gsl with external cblas provided by (virtual/cblas) instead of shipped internal version
+sci-libs/itk:itkv3compat - Enable compatibility with ITK version 3
+sci-libs/itk:review - Enable compilation of methods under review
+sci-libs/itk:vtkglue - PLEASE FIX MY DESCRIPTION
+sci-libs/lapack-reference:int64 - Build the 64 bits integer library
 sci-libs/lapack-reference:xblas - Build LAPACK with extra precision (needs sci-libs/xblas)
+sci-libs/lapacke-reference:tmg - Build LAPACKE with a Test Matrix Generator library
 sci-libs/lapacke-reference:xblas - Build LAPACKE with extra precision (needs sci-libs/xblas)
-sci-libs/levmar:plasma - Use the multi-threaded sci-libs/plasma library for linear algebra
 sci-libs/libfac:singular - Automatically generated description for singular
+sci-libs/libgeodecomp:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDASimulator and CUDAStepper)
+sci-libs/libgeodecomp:hpx - Activates the HPX backend as an alternative to the usual MPI backends.
+sci-libs/libgeodecomp:opencl - Builds those plugins which can offload to OpenCL devices.
+sci-libs/libgeodecomp:opencv - Some input components can read from cameras etc. via OpenCV
+sci-libs/libgeodecomp:qt4 - Adds the QTWidgetWriter, which allows in situ visualization of a running simulation.
+sci-libs/libgeodecomp:scotch - Optinally use Scotch for domain decomposition.
+sci-libs/libgeodecomp:visit - Add in situ visualization for big simulations via VisIt.
+sci-libs/libsc:romio - Build with support for the ROMIO MPI-IO component
 sci-libs/lwpr:octave - Add sci-mathematics/octave support
-sci-libs/magma:fermi - Compile for GPU NVIDIA Fermi family (2.x cards)
-sci-libs/magma:tesla - Compile for GPU NVIDIA Tesla family (1.x cards)>
-sci-libs/mumps:metis - Enable ordering with METIS (sci-libs/metis, sci-libs/parmetis)
-sci-libs/mumps:scotch - Enable ordering with sci-libs/scotch
+sci-libs/nexus:cbf - Support for Crystallographic Binary Format files with sci-libs/cbflib
+sci-libs/nexus:doc - Generate library documentation with app-doc/doxygen
+sci-libs/nexus:fortran - Build the Fortran bindings
+sci-libs/nexus:guile - Build the Scheme bindings
+sci-libs/nexus:java - Build the Java bindings
+sci-libs/nexus:python - Build the Python bindings
+sci-libs/nexus:swig - Generate bindings with dev-lang/swig
+sci-libs/nexus:tcl - Build the TCL bindings
+sci-libs/nexus:xml - Allow using the verbose XML representation of NeXus data
+sci-libs/nibabel:dicom - Adds limited read support for the DICOM imaging format.
 sci-libs/oasa:cairo - Add support for Cairo graphics library using dev-python/pycairo
 sci-libs/openblas:dynamic - Build dynamic architecture detection at run time (for multi targets)
-sci-libs/openblas:incblas - Build the CBLAS interface
 sci-libs/openblas:int64 - Build the 64 bits integer library
+sci-libs/p4est:romio - Build with support for the ROMIO MPI-IO component
+sci-libs/p4est:vtk-binary - Enable binary vtk output. If disabled vtk files will be written in ASCII text format.
 sci-libs/pagmo:kepler - Automatically generated description for kepler
 sci-libs/pagmo:nlopt - Automatically generated description for nlopt
 sci-libs/parmetis:double-precision - Floating-point operation done as double precision
 sci-libs/parmetis:int64 - Build the 64 bits integer library (needed for > 2^31 vertices)
-sci-mathematics/Macaulay2:optimization - Accept upstream's choices for -O option, i.e. -O3 almost everywhere.
-sci-mathematics/algae:intel - Use icc as c compiler
-sci-mathematics/apron:ppl - Enable optional interface to the Parma Polyhedra Library
+sci-libs/pastix:int64 - Build the 64 bits integer library
+sci-libs/pastix:starpu - Build and link with dev-libs/starpu
+sci-libs/scikits_image:freeimage - Enable support for image i/o via media-libs/freeimage
+sci-libs/trilinos:adolc - Add support for adolc (sci-libs/adolc)
+sci-libs/trilinos:arprec - Add support for arprec (sci-libs/arprec)
+sci-libs/trilinos:boost - Add support for boost (dev-libs/boost)
+sci-libs/trilinos:clp - Add support for clp (sci-libs/coinor-clp)
+sci-libs/trilinos:cppunit - Add support for ()
+sci-libs/trilinos:cuda - Add support for cuda (dev-util/nvidia-cuda-toolkit)
+sci-libs/trilinos:eigen - Add support for eigen (dev-cpp/eigen)
+sci-libs/trilinos:glpk - Add support for ()
+sci-libs/trilinos:gtest - Add support for gtest (dev-cpp/gtest)
+sci-libs/trilinos:hdf5 - Add support for hdf5 (sci-libs/hdf5)
+sci-libs/trilinos:hwloc - Add support for hwloc (sys-apps/hwloc)
+sci-libs/trilinos:hypre - Add support for hypre (sci-libs/hypre)
+sci-libs/trilinos:matio - Add support for matio (sci-libs/matio)
+sci-libs/trilinos:metis - Add support for metis (sci-libs/(par)metis)
+sci-libs/trilinos:mkl - Add support for mkl (sci/libs/mkl)
+sci-libs/trilinos:mumps - Add support for mumps (sci-libs/mumps)
+sci-libs/trilinos:netcdf - Add support for netcdf (sci-libs/netcdf)
+sci-libs/trilinos:petsc - Add support for petsc (sci-mathematics/petsc)
+sci-libs/trilinos:qd - Add support for qd (sci-libs/qd)
+sci-libs/trilinos:scalapack - Add support for scalapack (virtual/scalapack)
+sci-libs/trilinos:scotch - Add support for scotch (sci-libs/scotch)
+sci-libs/trilinos:sparse - Add support for sparse matrix solvers (sci-libs/umfpack)
+sci-libs/trilinos:superlu - Add support for superlu (sci-libs/superlu)
+sci-libs/trilinos:taucs - Add support for taucs (sci-libs/taucs)
+sci-libs/trilinos:tbb - Add support for threading building blocks library (dev-cpp/tbb)
+sci-libs/trilinos:tvmet - Add support for tvmet (dev-libs/tvmet)
+sci-libs/trilinos:umfpack - Add support for umfpack (sci-libs/umfpack)
+sci-libs/trilinos:yaml - Add support for yaml (dev-cpp-yaml)
+sci-libs/xblas:int64 - Build the 64 bits integer library
+sci-mathematics/Macaulay2:optimization - Disable to build with -O0 for debugging.
+sci-mathematics/acl2:books - build community books, the canonical collection of open-source libraries
+sci-mathematics/apron:ppl - Add support for dev-libs/ppl
 sci-mathematics/dolfin:cgal - Adds support for geometric algorithms with sci-mathematics/cgal
 sci-mathematics/dolfin:cholmod - Adds support for sparse Cholesky factorization with sci-libs/cholmod
 sci-mathematics/dolfin:parmetis - Adds support for parallel graph partitioning with sci-libs/parmetis
 sci-mathematics/dolfin:scotch - Adds support for graph partitioning with sci-libs/scotch
 sci-mathematics/dolfin:umfpack - Adds support for sparse solving with sci-libs/umfpack
-sci-mathematics/frama-c:apron - ?apron?
-sci-mathematics/frama-c:gtk - ?gtk?
-sci-mathematics/frama-c:why - ?why?
 sci-mathematics/gambit:X - Enable gui support using wxWidgets.
 sci-mathematics/gap:xtom - Automatically generated description for xtom
-sci-mathematics/giac:fltk - ?fltk?
 sci-mathematics/htk:hdecode - Install HDecode, a large vocabulary word recogniser
 sci-mathematics/htk:hlmtools - Install the tools for manipulation of language models
 sci-mathematics/htk:hslab - Install HSLab a label editor for speech label manipulation
 sci-mathematics/htk:htkbook - Build the HTK documentation (HTK Book)
 sci-mathematics/netgen:opencascade - Enable OpenCASCADE support
 sci-mathematics/petsc:afterimage - Use Afterstep image library (media-libs/libafterimage)
+sci-mathematics/petsc:boost - Use boost (dev-libs/boost)
 sci-mathematics/petsc:complex-scalars - Make scalars complex
 sci-mathematics/petsc:hypre - Use HYPRE (sci-mathematics/hypre) and for preconditioning
-sci-mathematics/petsc:metis - Use METIS (sci-libs/parmetis) for partitioning
+sci-mathematics/petsc:mumps - PLEASE FIX MY DESCRIPTION
+sci-mathematics/petsc:scotch - PLEASE FIX MY DESCRIPTION
 sci-mathematics/petsc:sparse - Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization
 sci-mathematics/petsc:superlu - Use superlu (sci-libs/superlu) for preconditioning
-sci-mathematics/polymake:libpolymake - Build the polymake library to build applications using the C++ interface.
-sci-mathematics/rstudio:desktop - Build the QT4 desktop interface
-sci-mathematics/rstudio:server - Build and install the RStudio server
+sci-mathematics/scilab:emf - Add suport for exporting to emf files
 sci-mathematics/scilab:gui - Build the Java base graphical interface
 sci-mathematics/scilab:matio - Enable support for MATLAB file through sci-libs/matio
 sci-mathematics/scilab:umfpack - Adds support for sparse solving with sci-libs/umfpack
 sci-mathematics/scilab:xcos - Enable building hybrid dynamic systems modeler and simulator Xcos
-sci-mathematics/why:apron - ?apron?
-sci-mathematics/why:coq - ?coq?
-sci-mathematics/why:gappa - ?gappa?
-sci-mathematics/why:gtk - ?gtk?
-sci-mathematics/why:jessie - ?jessie?
-sci-mathematics/why:pff - ?pff?
+sci-mathematics/why:apron - Use sci-mathematics/apron library for abstract interpretation
+sci-mathematics/why:coq - Add sci-mathematics/coq support
+sci-mathematics/why:float - Add sci-mathematics/flocq support
+sci-mathematics/why:frama-c - Add sci-mathematics/frama-c support
+sci-mathematics/why:gappa - Add sci-mathematics/gappalib-coq support
+sci-mathematics/why:pff - Add sci-mathematics/pff support
+sci-mathematics/why:why3 - Add sci-mathematics/why3 support
+sci-mathematics/why3:float - Add sci-mathematics/flocq support
+sci-mathematics/why3:frama-c - Enable Frama-C plugin
+sci-misc/elmer-gui:bundled_netgen - Use bundled version of sci-mathematics/netgen
+sci-misc/elmer-gui:matc - Enables sci-libs/matc support
+sci-misc/elmer-gui:opencascade - Enable sci-libs/opencascade support
+sci-misc/elmer-gui:qwt - Enables x11-libs/qwt support
+sci-misc/elmer-gui:vtk - Enables sci-libs/vtk support
 sci-misc/hfst:foma - Add optional support for foma backend library (sci-misc/foma)
 sci-misc/hfst:glib - Parse UTF-8 and collate unicode using glib instead of homebrewn methods
 sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-misc/openfst)
@@ -161,58 +327,107 @@ sci-misc/opennlp-tools:models - Automatically generated description for models
 sci-misc/salome-kernel:numpy - Enable support for dev-python/numpy
 sci-misc/salome-med:metis - Add support for metis
 sci-misc/salome-med:scotch - Add support for scotch
+sci-physics/abinit:atompaw - Enable support for atompaw, a Projector Augmented Waves atomic data generator
+sci-physics/abinit:bigdft - Enable support for BigDFT, DFT package using wavelet basis set
 sci-physics/abinit:cuda - Enable support for nVidia CUDA
 sci-physics/abinit:cuda-double - Enable support for double precision nVidia CUDA
-sci-physics/abinit:fftw-threads - Use the threaded version of sci-libs/fftw
+sci-physics/abinit:etsf_io - Enable support for reading and writing the European Theoretical Spectroscopy facility (ETSF) file format.
+sci-physics/abinit:fftw-mpi - Use the MPI version of sci-libs/fftw (always with either openMP or pthreads too)
+sci-physics/abinit:fftw-threads - Use the threaded (openMP or pthreads) version of sci-libs/fftw
 sci-physics/abinit:fox - Enable support for FoX Fortran XML library
-sci-physics/abinit:gui - Build the abinit GUI (requires java)
+sci-physics/abinit:levmar - Enable support for sci-libs/levmar, the Levenberg-Marquardt least-squares optimisation
 sci-physics/abinit:libabinit - Build the libabinit used by sci-libs/bigdft (usage not tested yet, circular dependency not resolved)
-sci-physics/abinit:vdwxc - Activate van der Waals exchange-correlation
-sci-physics/atompaw:libxc - Use libxc for something
+sci-physics/abinit:libxc - Enable support for libxc, an exchange-correlation potentials library
+sci-physics/abinit:lotf - Activate the Learn on The Fly method (LOTF) for Molecular Dynamics
+sci-physics/abinit:scalapack - Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing
+sci-physics/abinit:scripts - Install helper scripts, mostly Python
+sci-physics/abinit:vdwxc - Activate van der Waals exchange-correlation correction. Since 7.4.0 no longer optional
+sci-physics/abinit:wannier - Enable support for wannier90, a maximally localized Wannier functions (MLWFs) calculator
+sci-physics/atompaw:libxc - Enable support for libxc, an exchange-correlation potentials library
+sci-physics/atompaw:longplot - Patch the sources to plot functions all over the space considered, not just up to the matching radius plus 50 grid points. May be useless or even harmful.
+sci-physics/bigdft:cuda - Enable support for nVidia CUDA GPU acceleration
+sci-physics/bigdft:etsf_io - Enable support for reading and writing the European Theoretical Spectroscopy facility (ETSF) file format.
+sci-physics/bigdft:glib - Compile with GLib Object System support
+sci-physics/bigdft:opencl - Enable support for OpenCL GPU acceleration
+sci-physics/bigdft:scalapack - Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing
 sci-physics/elk:libxc - Use sci-libs/libxc library of exchange-correlation functionals by ETSF.
+sci-physics/elk:perl - Install perl scripts.
+sci-physics/elk:python - Install python scripts.
+sci-physics/espresso:cuda - Enable cuda support
 sci-physics/espresso:examples - Installs the examples
 sci-physics/espresso:packages - Installs extra subpackages
-sci-physics/root:c++0x - Build ROOT using the C++11 standard. Not supported, requires sys-devel/gcc>=4.7.0
+sci-physics/geant-vmc:g4root - Build G4Root (interface for GEANT4 simulation with a ROOT geometry)
+sci-physics/geant-vmc:geant3 - Build with Geant4 G3toG4 library
+sci-physics/geant-vmc:mtroot - Build MTRoot (provides ROOT IO manager classes with multi-threading support)
+sci-physics/geant-vmc:vgm - Enable the Virtual Geometry Model (sci-physics/vgm)
+sci-physics/herwig++:c++11 - Build Herwig++ using the C++11 standard. Experimental feature, not for production use.
+sci-physics/herwig++:fastjet - Adds support for sci-physics/fastjet
+sci-physics/hoomd-blue:cuda - Enable cuda non-bonded kernels
+sci-physics/mc-tester:hepmc - Compile sci-physics/hepmc interface
 sci-physics/root:fits - Support for images and data from FITS files with sci-libs/cfitsio
 sci-physics/root:geocad - Enable ROOT-CAD interface using sci-libs/opencascade
-sci-physics/root:htmldoc - Generate html documentation
-sci-physics/root:llvm - Build the new cling interactive interpreter based on sys-devel/llvm
+sci-physics/root:http - Enable http server support including but not limited to fastcgi support
 sci-physics/root:math - Build all math related libraries plugins, needs sci-libs/gsl
 sci-physics/root:pythia6 - Build the interface for sci-physics/pythia version 6.x
 sci-physics/root:pythia8 - Build the interface for sci-physics/pythia version 8.x
-sci-physics/root:reflex - Build the reflection database for the C++ interpreter
 sci-physics/root:xrootd - Build the interface for net-libs/xrootd
+sci-physics/tauola:hepmc - Compile sci-physics/hepmc interface
+sci-physics/tauola:tau-spinner - Compile with TauSpinner library
+sci-physics/thepeg:fastjet - Adds support for sci-physics/fastjet
+sci-physics/thepeg:hepmc - Adds support for High Energy Physics Monte Carlo Generators sci-physics/hepmc
+sci-physics/thepeg:lhapdf - Adds support for sci-physics/lhapdf
+sci-physics/thepeg:rivet - Adds support for sci-physics/rivet
+sci-physics/vgm:geant4 - Enable interaction with Geant4(sci-physics/geant:4)
+sci-physics/vgm:root - Enable interactions with ROOT (sci-physics/root)
+sci-physics/yoda:root - Adds support for sci-physics/root
 sci-visualization/gnuplot:bitmap - Enable dot-matrix printers and pbm terminal
+sci-visualization/gnuplot:compat - Enable backwards compatibility with version 4 syntax
 sci-visualization/gnuplot:gd - Add support for media-libs/gd. Needed for GIF, JPEG, and PNG image output.
-sci-visualization/gnuplot:thin-splines - Enable thin plate splines
+sci-visualization/gnuplot:libcerf - Enable special functions from sci-libs/libcerf
+sci-visualization/mantid:doc - Generate documentation with app-doc/doxygen, QT Assistant etc
+sci-visualization/mantid:opencascade - Use OpenCascade to show 3D models of instruments
+sci-visualization/mantid:opencl - Use OpenCL to accelerate calculations
+sci-visualization/mantid:paraview - Enable the Visualisation and Analysis Toolkit ExtensionS (VATES)
+sci-visualization/mantid:tcmalloc - Use thread-caching malloc
 sci-visualization/nodemon:pbs - Enable support for the Portable Batch System.
-sci-visualization/paraview:adaptive - Enable the adaptive paraview application
-sci-visualization/paraview:boost - Add support for boost
-sci-visualization/paraview:cg - Add support for nvidia's cg shaders
-sci-visualization/paraview:coprocessing - Enable the coprocessing infrastructure which is mainly useful in the context of clusters
-sci-visualization/paraview:gui - Build paraview's gui not just the server
-sci-visualization/paraview:mysql - Build support for MySQL data item in the XDMF format
-sci-visualization/paraview:nvcontrol - Add NVCONTROL support for OpenGL options
-sci-visualization/paraview:plugins - Build and install additional plugins
-sci-visualization/paraview:streaming - Enable streaming paraview application
-sci-visualization/paraview:webkit - Built support for qt-webkit in vtk
 sci-visualization/v_sim:abinit - Add support for ABINIT file formats sci-physics/abinit
 sci-visualization/v_sim:cube - Add support plug-in support for Cube files (densities and structures)
 sci-visualization/v_sim:openbabel - Add support for ABINIT file formats sci-chemistry/openbabel
 sci-visualization/v_sim:xsf - plug-in support for files that follow the XCrysDen format for structural positions and densities
-sys-cluster/condor:classads - Enable the Condor's classified advertisement language
-sys-cluster/condor:drmaa - Enable the Distributed Resource Management Application API
-sys-cluster/condor:gcb - Enable condor to communicate over firewall/NAT
-sys-cluster/condor:kbdd - Enable the Condor Keyboard Daemon to monitor logged in X users for activity
+sys-cluster/hpx:jemalloc - Use dev-libs/jemalloc for memory allocation
+sys-cluster/hpx:papi - Use dev-libs/papi for NaCl
+sys-cluster/hpx:perftools - Use dev-util/google-perftools for memory allocation
+sys-cluster/hpx:tbb - Use dev-cpp/tbb for memory allocation
+sys-cluster/htcondor:X - Enable the HTCondor Keyboard Daemon to monitor logged in X users for activity
+sys-cluster/htcondor:boinc - Enable backfill with BOINC jobs when the cluster is not being used
+sys-cluster/htcondor:cgroup - Use dev-libs/libcgroup for kernel control groups
+sys-cluster/htcondor:contrib - Build contrib modules
+sys-cluster/htcondor:dmtcp - Use sys-apps/dmtcp for checkpointing
+sys-cluster/htcondor:libvirt - Use app-emulation/libvirt for virtualisation
+sys-cluster/htcondor:management - Use net-libs/qmf for management
+sys-cluster/htcondor:minimal - Don't support standard universe jobs
+sys-cluster/lustre:client - Enable kernel client modules
+sys-cluster/lustre:liblustre - Enable building of liblustre
+sys-cluster/lustre:server - Enable kernels server modules
+sys-cluster/lustre:tests - Enable installation of tests
+sys-cluster/lustre:urandom - Enable use of urandom
+sys-cluster/lustre:utils - Enable lustre utils
+sys-cluster/mpich:mpi-threads - Enable MPI_THREAD_MULTIPLE
+sys-cluster/mpich:romio - Build the ROMIO MPI-IO component
 sys-cluster/mpich2:mpi-threads - Enable MPI_THREAD_MULTIPLE
 sys-cluster/mpich2:romio - Build the ROMIO MPI-IO component
 sys-cluster/mvapich2:large-cluster - Automatically generated description for large-cluster
 sys-cluster/mvapich2:medium-cluster - Automatically generated description for medium-cluster
 sys-cluster/mvapich2:romio - Automatically generated description for romio
+sys-cluster/openmpi:cma - Enable the CMA (Cross Memory Attach) MCA
+sys-cluster/openmpi:cuda - Add GPU direct support
 sys-cluster/openmpi:heterogeneous - Enable features required for heterogeneous platform support
-sys-cluster/openmpi:infiniband - Enable infiniband support
 sys-cluster/openmpi:mpi-threads - Enable MPI_THREAD_MULTIPLE
-sys-cluster/openmpi:pbs - Add support for the Portable Batch System (PBS)
+sys-cluster/openmpi:numa - Enable numactl to allow binding processes to CPUs
 sys-cluster/openmpi:romio - Build the ROMIO MPI-IO component
 sys-cluster/openmpi:vt - Enable bundled VampirTrace support
+virtual/blas:int64 - Add eselect module for blas libraries built with 64 bits integer ABI
+virtual/cblas:int64 - Add eselect module for cblas libraries built with 64 bits integer ABI
+virtual/lapack:int64 - Add eselect module for lapack libraries built with 64 bits integer ABI
 virtual/mpi:romio - Enable romio, a high-performance portable MPI-IO
+x11-libs/agg:gpc - Enable gpc polygon clipper library

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

[Justin Lecher]

commit:     1774bc7ba98159438cc17d77450a5bc64134cdd8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  9 08:01:48 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep  9 08:01:48 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1774bc7b

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 855f59c..8587810 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -98,7 +98,6 @@ sci-biology/ncbi-tools++:xalan - Undocumented USE
 sci-biology/ncbi-tools++:xerces - Undocumented USE
 sci-biology/ncbi-tools++:xslt - Undocumented USE
 sci-biology/sga:jemalloc - Use dev-libs/jemalloc
-sci-biology/tophat:bam - Compile support for the BAM format
 sci-chemistry/avogadro2:rpc - Enable RPC server
 sci-chemistry/ball:cuda - Include cuda support
 sci-chemistry/ball:sql - Include SQL database support

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

[Justin Lecher]

commit:     ef4fc621e93da5342bccf49c8065d236df670259
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 14 08:18:49 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 14 08:18:49 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ef4fc621

Update local USE descriptions

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 8587810..189285e 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -54,11 +54,6 @@ dev-util/amdapp:examples - Build the OpenCL example programs
 dev-util/nvidia-cuda-gdk:healthmon - Install nvidia-healthmon.
 dev-util/nvidia-cuda-gdk:nvml - Install the NVIDIA Managment Library.
 dev-util/nvidia-cuda-gdk:nvvs - Install the NVIDIA Validation Suite.
-dev-util/nvidia-cuda-sdk:cuda - Build CUDA binaries.
-dev-util/nvidia-cuda-sdk:opencl - Build OpenCL binaries.
-dev-util/nvidia-cuda-toolkit:debugger - Installs the CUDA debugger.
-dev-util/nvidia-cuda-toolkit:eclipse - Install the dev-util/eclipse-sdk plugins
-dev-util/nvidia-cuda-toolkit:profiler - Installs the NVIDIA CUDA visual profiler.
 media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled)
 media-gfx/librecad:3d - Require all 2D coordinates stored as 3D
 media-gfx/librecad:tools - Build additional tool programs: tff2lff
@@ -169,6 +164,7 @@ sci-libs/cblas-reference:int64 - Build the 64 bits integer library
 sci-libs/clblas:client - Build a command line clBLAS client program.
 sci-libs/clblas:ktest - A command line tool for testing single clBLAS kernel.
 sci-libs/clblas:performance - Copy performance scripts that can measure and graph performance.
+sci-libs/clfft:client - Build a command line clFFT client program.
 sci-libs/clrng:client - Build a command line clRNG client program.
 sci-libs/dealii:arpack - Adds support for ARPACK (sci-libs/arpack)
 sci-libs/dealii:c++11 - Compile the library with -std=c++11

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

[Justin Lecher]

commit:     c5aa58d1bbc655bafb397cfba6d98e25c840a752
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 15:47:25 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 15:48:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c5aa58d1

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 189285e..1108aca 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -148,9 +148,10 @@ sci-libs/armadillo:atlas - Link with sci-libs/atlas libraries for cblas and clap
 sci-libs/armadillo:mkl - Use matrix allocation from the Intel MKL sci-libs/mkl
 sci-libs/armadillo:superlu - Use SuperLU for sparse linear equation solving sci-libs/superlu
 sci-libs/armadillo:tbb - Use matrix allocation from the Threads Building Blocks dev-cpp/tbb
-sci-libs/arrayfire:cpu - Enable CPU Build.
-sci-libs/arrayfire:cuda - Enable CUDA Build.
-sci-libs/arrayfire:opencl - Enable OpenCL Build.
+sci-libs/arrayfire:cpu - Build CPU backend.
+sci-libs/arrayfire:cuda - Build CUDA backend.
+sci-libs/arrayfire:graphics - Build with Forge graphics.
+sci-libs/arrayfire:opencl - Build OpenCL backend.
 sci-libs/asl:matio - Matlab support with sci-libs/matio
 sci-libs/atlas:generic - Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)
 sci-libs/bigdft-abi:cuda - Enable support for nVidia CUDA

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

[Justin Lecher]

commit:     4e360b304237afc74ff81533f141e9c168acde87
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 19:05:53 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 19:05:53 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e360b30

Add local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 1108aca..dc77283 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -151,6 +151,7 @@ sci-libs/armadillo:tbb - Use matrix allocation from the Threads Building Blocks
 sci-libs/arrayfire:cpu - Build CPU backend.
 sci-libs/arrayfire:cuda - Build CUDA backend.
 sci-libs/arrayfire:graphics - Build with Forge graphics.
+sci-libs/arrayfire:nonfree - Build ArrayFire nonfree algorithms.
 sci-libs/arrayfire:opencl - Build OpenCL backend.
 sci-libs/asl:matio - Matlab support with sci-libs/matio
 sci-libs/atlas:generic - Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)

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

[Justin Lecher]

commit:     937967a6aceb74fc7f6cf807c4f6984f3672b70b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 22 07:27:58 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 22 07:27:58 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=937967a6

Update local USe description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index dc77283..6d27954 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -32,12 +32,6 @@ dev-lang/path64:valgrind - Support compiler debugging with dev-util/valgrind
 dev-lang/pgi:acml - Install AMD's core math library.
 dev-lang/pgi:cuda - Install PGI's CUDA components (e.g. for OpenACC)
 dev-lang/pgi:java - Install a PGI-tuned JRE.
-dev-libs/boost:context - Build and install the Boost.Context library and all other Boostlibraries that depends on it
-dev-libs/boost:debug - Build and install only the debug version of the Boost libraries. Only enable this flag if you're developing against boost.
-dev-libs/boost:doc - Install the full API documentation documentation. This takes over 200MB of extra disk space.
-dev-libs/boost:nls - Build libboost_locale. This library requires compatible C library interfaces, which might not be provided by uClibc or other embedded libraries.
-dev-libs/boost:threads - Build multi-thread-compatible libraries instead of single-threaded only.
-dev-libs/boost:tools - Build and install the boost tools (bcp, quickbook, inspect, wave)
 dev-libs/libflatarray:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator)
 dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
 dev-ml/zarith:mpir - Use sci-libs/mpir for arbitrary precision integer arithmetic
@@ -270,12 +264,10 @@ sci-libs/trilinos:superlu - Add support for superlu (sci-libs/superlu)
 sci-libs/trilinos:taucs - Add support for taucs (sci-libs/taucs)
 sci-libs/trilinos:tbb - Add support for threading building blocks library (dev-cpp/tbb)
 sci-libs/trilinos:tvmet - Add support for tvmet (dev-libs/tvmet)
-sci-libs/trilinos:umfpack - Add support for umfpack (sci-libs/umfpack)
 sci-libs/trilinos:yaml - Add support for yaml (dev-cpp-yaml)
 sci-libs/xblas:int64 - Build the 64 bits integer library
 sci-mathematics/Macaulay2:optimization - Disable to build with -O0 for debugging.
 sci-mathematics/acl2:books - build community books, the canonical collection of open-source libraries
-sci-mathematics/apron:ppl - Add support for dev-libs/ppl
 sci-mathematics/dolfin:cgal - Adds support for geometric algorithms with sci-mathematics/cgal
 sci-mathematics/dolfin:cholmod - Adds support for sparse Cholesky factorization with sci-libs/cholmod
 sci-mathematics/dolfin:parmetis - Adds support for parallel graph partitioning with sci-libs/parmetis
@@ -321,9 +313,6 @@ sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-mi
 sci-misc/hfst:sfst - Add optional support for sfst backend library (sci-misc/sfst)
 sci-misc/hfst:xml - Include parsers for grammars and formats that require XML support
 sci-misc/opennlp-tools:models - Automatically generated description for models
-sci-misc/salome-kernel:numpy - Enable support for dev-python/numpy
-sci-misc/salome-med:metis - Add support for metis
-sci-misc/salome-med:scotch - Add support for scotch
 sci-physics/abinit:atompaw - Enable support for atompaw, a Projector Augmented Waves atomic data generator
 sci-physics/abinit:bigdft - Enable support for BigDFT, DFT package using wavelet basis set
 sci-physics/abinit:cuda - Enable support for nVidia CUDA
@@ -370,10 +359,6 @@ sci-physics/root:pythia8 - Build the interface for sci-physics/pythia version 8.
 sci-physics/root:xrootd - Build the interface for net-libs/xrootd
 sci-physics/tauola:hepmc - Compile sci-physics/hepmc interface
 sci-physics/tauola:tau-spinner - Compile with TauSpinner library
-sci-physics/thepeg:fastjet - Adds support for sci-physics/fastjet
-sci-physics/thepeg:hepmc - Adds support for High Energy Physics Monte Carlo Generators sci-physics/hepmc
-sci-physics/thepeg:lhapdf - Adds support for sci-physics/lhapdf
-sci-physics/thepeg:rivet - Adds support for sci-physics/rivet
 sci-physics/vgm:geant4 - Enable interaction with Geant4(sci-physics/geant:4)
 sci-physics/vgm:root - Enable interactions with ROOT (sci-physics/root)
 sci-physics/yoda:root - Adds support for sci-physics/root

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

[Justin Lecher]

commit:     fa08cb9e8017787a48a4ac93eedfdff315eac6e5
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 23 08:43:25 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 23 08:43:25 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fa08cb9e

Update local USE descriptions

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 6d27954..49ba621 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -312,7 +312,6 @@ sci-misc/hfst:glib - Parse UTF-8 and collate unicode using glib instead of homeb
 sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-misc/openfst)
 sci-misc/hfst:sfst - Add optional support for sfst backend library (sci-misc/sfst)
 sci-misc/hfst:xml - Include parsers for grammars and formats that require XML support
-sci-misc/opennlp-tools:models - Automatically generated description for models
 sci-physics/abinit:atompaw - Enable support for atompaw, a Projector Augmented Waves atomic data generator
 sci-physics/abinit:bigdft - Enable support for BigDFT, DFT package using wavelet basis set
 sci-physics/abinit:cuda - Enable support for nVidia CUDA

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

[Justin Lecher]

commit:     c6f4e833dae426ea34cf77db288a047520dc24ce
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 24 06:12:57 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Sep 24 06:12:57 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c6f4e833

Add local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 6d27954..49ba621 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -312,7 +312,6 @@ sci-misc/hfst:glib - Parse UTF-8 and collate unicode using glib instead of homeb
 sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-misc/openfst)
 sci-misc/hfst:sfst - Add optional support for sfst backend library (sci-misc/sfst)
 sci-misc/hfst:xml - Include parsers for grammars and formats that require XML support
-sci-misc/opennlp-tools:models - Automatically generated description for models
 sci-physics/abinit:atompaw - Enable support for atompaw, a Projector Augmented Waves atomic data generator
 sci-physics/abinit:bigdft - Enable support for BigDFT, DFT package using wavelet basis set
 sci-physics/abinit:cuda - Enable support for nVidia CUDA

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

[Justin Lecher]

commit:     0817705d6ba528d15e6ae591e8c023430e660283
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 10 14:10:52 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 10 14:10:52 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0817705d

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 49ba621..f1e49d2 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -147,6 +147,7 @@ sci-libs/arrayfire:cuda - Build CUDA backend.
 sci-libs/arrayfire:graphics - Build with Forge graphics.
 sci-libs/arrayfire:nonfree - Build ArrayFire nonfree algorithms.
 sci-libs/arrayfire:opencl - Build OpenCL backend.
+sci-libs/arrayfire:unified - Build Backend-Independent API.
 sci-libs/asl:matio - Matlab support with sci-libs/matio
 sci-libs/atlas:generic - Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)
 sci-libs/bigdft-abi:cuda - Enable support for nVidia CUDA
@@ -238,6 +239,7 @@ sci-libs/parmetis:int64 - Build the 64 bits integer library (needed for > 2^31 v
 sci-libs/pastix:int64 - Build the 64 bits integer library
 sci-libs/pastix:starpu - Build and link with dev-libs/starpu
 sci-libs/scikits_image:freeimage - Enable support for image i/o via media-libs/freeimage
+sci-libs/symengine:boost - Add support for boost (dev-libs/boost)
 sci-libs/trilinos:adolc - Add support for adolc (sci-libs/adolc)
 sci-libs/trilinos:arprec - Add support for arprec (sci-libs/arprec)
 sci-libs/trilinos:boost - Add support for boost (dev-libs/boost)

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

[Justin Lecher]

commit:     667950a8c29209eff73ae066c4e473dddfd13cf9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Oct 15 17:10:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Oct 15 17:10:15 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=667950a8

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index f1e49d2..5c505f4 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -58,6 +58,7 @@ sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plot
 sci-astronomy/scamp:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
 sci-astronomy/sextractor:modelfit - Enable profile model fitting, needs sci-libs/atlas and sci-libs/fftw
 sci-astronomy/zpeg:gdl - Install GDL/IDL plotting routines
+sci-biology/bowtie:tbb - Enables building bowtie with the Intel Threading Building Blocks from dev-cpp/tbb. This flag is recommended.
 sci-biology/discrover:cairo - Use Cairo for sequence logo plotting capabilities
 sci-biology/discrover:dreme - Enable usage of DREME from the MEME package for seeding
 sci-biology/discrover:lto - Compile with link-time optimization (LTO)

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

[Justin Lecher]

commit:     e33da5e9f3088a92695c340a0b8993263bb82793
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 17 07:43:55 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 17 07:43:55 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e33da5e9

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 5c505f4..f1e49d2 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -58,7 +58,6 @@ sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plot
 sci-astronomy/scamp:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
 sci-astronomy/sextractor:modelfit - Enable profile model fitting, needs sci-libs/atlas and sci-libs/fftw
 sci-astronomy/zpeg:gdl - Install GDL/IDL plotting routines
-sci-biology/bowtie:tbb - Enables building bowtie with the Intel Threading Building Blocks from dev-cpp/tbb. This flag is recommended.
 sci-biology/discrover:cairo - Use Cairo for sequence logo plotting capabilities
 sci-biology/discrover:dreme - Enable usage of DREME from the MEME package for seeding
 sci-biology/discrover:lto - Compile with link-time optimization (LTO)

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

[Justin Lecher]

commit:     eee26b8821732bfd2b7de60b23b23751328bf8a3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 10 10:52:00 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Nov 10 10:52:00 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=eee26b88

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index f1e49d2..a221265 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -58,6 +58,7 @@ sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plot
 sci-astronomy/scamp:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
 sci-astronomy/sextractor:modelfit - Enable profile model fitting, needs sci-libs/atlas and sci-libs/fftw
 sci-astronomy/zpeg:gdl - Install GDL/IDL plotting routines
+sci-biology/bru2nii:gui - Build graphical user interface
 sci-biology/discrover:cairo - Use Cairo for sequence logo plotting capabilities
 sci-biology/discrover:dreme - Enable usage of DREME from the MEME package for seeding
 sci-biology/discrover:lto - Compile with link-time optimization (LTO)
@@ -161,6 +162,7 @@ sci-libs/cblas-reference:int64 - Build the 64 bits integer library
 sci-libs/clblas:client - Build a command line clBLAS client program.
 sci-libs/clblas:ktest - A command line tool for testing single clBLAS kernel.
 sci-libs/clblas:performance - Copy performance scripts that can measure and graph performance.
+sci-libs/clfft:callback_client - Build a command line clFFT client program that tests callback functionality.
 sci-libs/clfft:client - Build a command line clFFT client program.
 sci-libs/clrng:client - Build a command line clRNG client program.
 sci-libs/dealii:arpack - Adds support for ARPACK (sci-libs/arpack)
@@ -239,6 +241,7 @@ sci-libs/parmetis:int64 - Build the 64 bits integer library (needed for > 2^31 v
 sci-libs/pastix:int64 - Build the 64 bits integer library
 sci-libs/pastix:starpu - Build and link with dev-libs/starpu
 sci-libs/scikits_image:freeimage - Enable support for image i/o via media-libs/freeimage
+sci-libs/scikits_image:pyamg - Enable support for algebraic solvers via dev-python/pyamg
 sci-libs/symengine:boost - Add support for boost (dev-libs/boost)
 sci-libs/trilinos:adolc - Add support for adolc (sci-libs/adolc)
 sci-libs/trilinos:arprec - Add support for arprec (sci-libs/arprec)

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

[Justin Lecher]

commit:     ed41a36ad9dd0ce72898060da7d4cf3b89a3aae5
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 13 09:38:41 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Nov 13 09:38:41 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ed41a36a

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index a221265..cefac74 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -119,7 +119,6 @@ sci-chemistry/openbabel:perl - Install Perl bindings.
 sci-chemistry/openbabel:python - Install Python bindings and PyBel.
 sci-chemistry/openbabel:ruby - Install Ruby bindings.
 sci-chemistry/openbabel:wxwidgets - Build Open Babel GUI.
-sci-chemistry/pymol:apbs - Pymol supprt for sci-chemistry/apbs
 sci-chemistry/pymol:web - Install Pymodule needed for web app support
 sci-chemistry/rosetta:boinc - compile rosetta as a rosetta@home client
 sci-chemistry/rosetta:boost - compile rosetta with boost supported code

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

[Justin Lecher]

commit:     217e4759c476bca33e35e124a6baf06f5b808a34
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 16 06:44:51 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 16 06:44:51 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=217e4759

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index a221265..cefac74 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -119,7 +119,6 @@ sci-chemistry/openbabel:perl - Install Perl bindings.
 sci-chemistry/openbabel:python - Install Python bindings and PyBel.
 sci-chemistry/openbabel:ruby - Install Ruby bindings.
 sci-chemistry/openbabel:wxwidgets - Build Open Babel GUI.
-sci-chemistry/pymol:apbs - Pymol supprt for sci-chemistry/apbs
 sci-chemistry/pymol:web - Install Pymodule needed for web app support
 sci-chemistry/rosetta:boinc - compile rosetta as a rosetta@home client
 sci-chemistry/rosetta:boost - compile rosetta with boost supported code

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

[Christoph Junghans]

commit:     b0a969fc203312521b3ad1c18b91e7493a279534
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 20 13:01:42 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Nov 20 13:01:42 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b0a969fc

Update local USE descriptions

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index cefac74..57e1cd6 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -67,6 +67,7 @@ sci-biology/discrover:rmathlib - Link to the standalone Rmathlib for statistical
 sci-biology/estscan:icc - Undocumented USE
 sci-biology/estscan:ifc - Undocumented USE
 sci-biology/exonerate-gff3:utils - Unknown
+sci-biology/hmmer:pvm - Add support for parallel virtual machine (sys-cluster/pvm)
 sci-biology/ncbi-blast+:boost - Undocumented USE
 sci-biology/ncbi-blast+:cppunit - Undocumented USE
 sci-biology/ncbi-blast+:freetype - Undocumented USE
@@ -316,6 +317,7 @@ sci-misc/hfst:glib - Parse UTF-8 and collate unicode using glib instead of homeb
 sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-misc/openfst)
 sci-misc/hfst:sfst - Add optional support for sfst backend library (sci-misc/sfst)
 sci-misc/hfst:xml - Include parsers for grammars and formats that require XML support
+sci-misc/kaldi:cuda - Build with CUDA support.
 sci-physics/abinit:atompaw - Enable support for atompaw, a Projector Augmented Waves atomic data generator
 sci-physics/abinit:bigdft - Enable support for BigDFT, DFT package using wavelet basis set
 sci-physics/abinit:cuda - Enable support for nVidia CUDA

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

[Justin Lecher]

commit:     ebad03e02bc8259366d85fd85047cc9f87dfca21
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 29 09:46:52 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Nov 29 09:46:52 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ebad03e0

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 57e1cd6..e095b83 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -36,10 +36,6 @@ dev-libs/libflatarray:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator
 dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
 dev-ml/zarith:mpir - Use sci-libs/mpir for arbitrary precision integer arithmetic
 dev-python/ffnet:matplotlib - Use matplotlib for drawing
-dev-python/ipython:matplotlib - Add support for dev-python/matplotlib
-dev-python/ipython:mongodb - Enable support for MongoDB via dev-python/pymongo
-dev-python/ipython:nbconvert - Enable support for converting notebooks to various formats using app-text/pandoc
-dev-python/ipython:notebook - Install requirements for the web notebook based on www-servers/tornado
 dev-python/pyhdf:szip - Allow to use sci-libs/szip for SZIP compression method in SDsetcompress()
 dev-python/ufl:scipy - Adds support for evaluating Bessel functions using dev-python/scipy
 dev-tex/pythontex:highlighting - PLEASE FIX MY DESCRIPTION

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

[Justin Lecher]

commit:     89bbf8ed02c91ee644b7cf4a9235ab67b1898ea1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  1 09:37:09 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Dec  1 09:37:23 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=89bbf8ed

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index e095b83..63c5088 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -194,7 +194,6 @@ sci-libs/gmsh:opencascade - Enable OpenCASCADE support
 sci-libs/gmsh:petsc - Enable sci-mathematics/petsc support
 sci-libs/gmsh:taucs - Enable sci-libs/taucs support
 sci-libs/gmsh:tetgen - Enable 3D delauny triangulation using tetgen lib
-sci-libs/gotoblas2:dynamic - Build dynamic architecture detection at run time (for multi targets)
 sci-libs/gotoblas2:incblas - Build the CBLAS interface
 sci-libs/gotoblas2:int64 - Build the 64 bits integer library
 sci-libs/gsl:cblas-external - Link gsl with external cblas provided by (virtual/cblas) instead of shipped internal version

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

[Justin Lecher]

commit:     ffd90e6017cacbb6648f3285b0e4b09f3f3a4e25
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  3 07:41:38 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec  3 07:41:38 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ffd90e60

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 63c5088..0bd80a8 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -200,6 +200,7 @@ sci-libs/gsl:cblas-external - Link gsl with external cblas provided by (virtual/
 sci-libs/itk:itkv3compat - Enable compatibility with ITK version 3
 sci-libs/itk:review - Enable compilation of methods under review
 sci-libs/itk:vtkglue - PLEASE FIX MY DESCRIPTION
+sci-libs/lapack-reference:deprecated - Build deprecated routines
 sci-libs/lapack-reference:int64 - Build the 64 bits integer library
 sci-libs/lapack-reference:xblas - Build LAPACK with extra precision (needs sci-libs/xblas)
 sci-libs/lapacke-reference:tmg - Build LAPACKE with a Test Matrix Generator library

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

[Justin Lecher]

commit:     d2eb76068f0affb96ee56f9964cd655b41f914be
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec  4 07:02:06 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec  4 07:02:06 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d2eb7606

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 0bd80a8..c57485c 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -147,6 +147,7 @@ sci-libs/arrayfire:opencl - Build OpenCL backend.
 sci-libs/arrayfire:unified - Build Backend-Independent API.
 sci-libs/asl:matio - Matlab support with sci-libs/matio
 sci-libs/atlas:generic - Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)
+sci-libs/atlas:ifko - Use iFKO to improve ATLAS performance (ATTENTION!!! Increases builtime enormously)
 sci-libs/bigdft-abi:cuda - Enable support for nVidia CUDA
 sci-libs/bigdft-abi:etsf_io - Enable support for reading and writing the European Theoretical Spectroscopy facility (ETSF) file format
 sci-libs/bigdft-abi:glib - Compile with GLib Object System support

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

[Justin Lecher]

commit:     c1e7253deb3950b1a7e6b429ca64e9d0b8942a46
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 13 12:28:35 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Dec 13 12:28:35 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c1e7253d

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index c57485c..3e06f58 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -146,6 +146,7 @@ sci-libs/arrayfire:nonfree - Build ArrayFire nonfree algorithms.
 sci-libs/arrayfire:opencl - Build OpenCL backend.
 sci-libs/arrayfire:unified - Build Backend-Independent API.
 sci-libs/asl:matio - Matlab support with sci-libs/matio
+sci-libs/atlas:deprecated - Build deprecated routines
 sci-libs/atlas:generic - Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)
 sci-libs/atlas:ifko - Use iFKO to improve ATLAS performance (ATTENTION!!! Increases builtime enormously)
 sci-libs/bigdft-abi:cuda - Enable support for nVidia CUDA

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

[Justin Lecher]

commit:     9c53144f557b7c1fe0e44b0693ef099f7d95f368
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 18 17:26:57 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 18 17:27:16 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c53144f

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 3e06f58..613facd 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -36,6 +36,7 @@ dev-libs/libflatarray:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator
 dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
 dev-ml/zarith:mpir - Use sci-libs/mpir for arbitrary precision integer arithmetic
 dev-python/ffnet:matplotlib - Use matplotlib for drawing
+dev-python/nilearn:plot - Adds optional dependency needed for plotting function subset.
 dev-python/pyhdf:szip - Allow to use sci-libs/szip for SZIP compression method in SDsetcompress()
 dev-python/ufl:scipy - Adds support for evaluating Bessel functions using dev-python/scipy
 dev-tex/pythontex:highlighting - PLEASE FIX MY DESCRIPTION

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

[Justin Lecher]

commit:     a13680689d4e3a9c5b056cb945a15ccdffb68970
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 21 10:38:28 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec 21 10:38:28 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1368068

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 613facd..7f77383 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -36,7 +36,6 @@ dev-libs/libflatarray:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator
 dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
 dev-ml/zarith:mpir - Use sci-libs/mpir for arbitrary precision integer arithmetic
 dev-python/ffnet:matplotlib - Use matplotlib for drawing
-dev-python/nilearn:plot - Adds optional dependency needed for plotting function subset.
 dev-python/pyhdf:szip - Allow to use sci-libs/szip for SZIP compression method in SDsetcompress()
 dev-python/ufl:scipy - Adds support for evaluating Bessel functions using dev-python/scipy
 dev-tex/pythontex:highlighting - PLEASE FIX MY DESCRIPTION
@@ -85,6 +84,7 @@ sci-biology/ncbi-tools++:sqlite3 - Add support for dev-db/sqlite:3
 sci-biology/ncbi-tools++:xalan - Undocumented USE
 sci-biology/ncbi-tools++:xerces - Undocumented USE
 sci-biology/ncbi-tools++:xslt - Undocumented USE
+sci-biology/nilearn:plot - Adds optional dependency needed for plotting function subset.
 sci-biology/sga:jemalloc - Use dev-libs/jemalloc
 sci-chemistry/avogadro2:rpc - Enable RPC server
 sci-chemistry/ball:cuda - Include cuda support

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

[Justin Lecher]

commit:     bdda4e7c8e98cff171453c0dad3c34b3098058b6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 28 16:11:51 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec 28 16:11:51 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bdda4e7c

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 7f77383..ad579d6 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -218,6 +218,7 @@ sci-libs/libgeodecomp:scotch - Optinally use Scotch for domain decomposition.
 sci-libs/libgeodecomp:visit - Add in situ visualization for big simulations via VisIt.
 sci-libs/libsc:romio - Build with support for the ROMIO MPI-IO component
 sci-libs/lwpr:octave - Add sci-mathematics/octave support
+sci-libs/mkl:int64 - Build the 64 bits integer library
 sci-libs/nexus:cbf - Support for Crystallographic Binary Format files with sci-libs/cbflib
 sci-libs/nexus:doc - Generate library documentation with app-doc/doxygen
 sci-libs/nexus:fortran - Build the Fortran bindings
@@ -412,8 +413,11 @@ sys-cluster/openmpi:mpi-threads - Enable MPI_THREAD_MULTIPLE
 sys-cluster/openmpi:numa - Enable numactl to allow binding processes to CPUs
 sys-cluster/openmpi:romio - Build the ROMIO MPI-IO component
 sys-cluster/openmpi:vt - Enable bundled VampirTrace support
+virtual/blacs:int64 - Add eselect module for blas libraries built with 64 bits integer ABI
 virtual/blas:int64 - Add eselect module for blas libraries built with 64 bits integer ABI
 virtual/cblas:int64 - Add eselect module for cblas libraries built with 64 bits integer ABI
 virtual/lapack:int64 - Add eselect module for lapack libraries built with 64 bits integer ABI
+virtual/lapacke:int64 - Add eselect module for blas libraries built with 64 bits integer ABI
 virtual/mpi:romio - Enable romio, a high-performance portable MPI-IO
+virtual/scalapack:int64 - Add eselect module for blas libraries built with 64 bits integer ABI
 x11-libs/agg:gpc - Enable gpc polygon clipper library

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

[Justin Lecher]

commit:     2172891ae686b906fbfb44475b9082768e62408b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 29 10:45:57 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Dec 29 10:45:57 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2172891a

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index ad579d6..78eb7fb 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -87,6 +87,7 @@ sci-biology/ncbi-tools++:xslt - Undocumented USE
 sci-biology/nilearn:plot - Adds optional dependency needed for plotting function subset.
 sci-biology/sga:jemalloc - Use dev-libs/jemalloc
 sci-chemistry/avogadro2:rpc - Enable RPC server
+sci-chemistry/avogadro2:vtk - include vtk support
 sci-chemistry/ball:cuda - Include cuda support
 sci-chemistry/ball:sql - Include SQL database support
 sci-chemistry/ball:webkit - Uses dev-qt/qt-webkit for drawing

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

[Justin Lecher]

commit:     0f45944404d54c4b92b44c48d3263f6cb4034585
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 29 19:07:59 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Dec 29 19:07:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0f459444

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 78eb7fb..8ba2c5c 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -86,8 +86,6 @@ sci-biology/ncbi-tools++:xerces - Undocumented USE
 sci-biology/ncbi-tools++:xslt - Undocumented USE
 sci-biology/nilearn:plot - Adds optional dependency needed for plotting function subset.
 sci-biology/sga:jemalloc - Use dev-libs/jemalloc
-sci-chemistry/avogadro2:rpc - Enable RPC server
-sci-chemistry/avogadro2:vtk - include vtk support
 sci-chemistry/ball:cuda - Include cuda support
 sci-chemistry/ball:sql - Include SQL database support
 sci-chemistry/ball:webkit - Uses dev-qt/qt-webkit for drawing

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

[Christoph Junghans]

commit:     372d0e6a6d2bfa53097e3ce975bc9ae6c38008be
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Jan  1 17:30:34 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan  1 17:30:34 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=372d0e6a

Update local USE description

Signed-off-by: Christoph Junghans <ottxor <AT> gentoo.org>

 profiles/use.local.desc | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 8ba2c5c..e64fe6d 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -24,6 +24,8 @@ dev-lang/berkeley_upc:sptr-struct - Use the 'struct' shared pointer representati
 dev-lang/berkeley_upc:sptr-symmetric - Enable 'symmetric' pointer variant where available (64-bit smp and shmem)
 dev-lang/berkeley_upc:udp - Support running over UDP
 dev-lang/conceptual:gui - Build the Java base graphical interface
+dev-lang/icc:eclipse - Install the dev-util/eclipse-sdk plugins
+dev-lang/idb:eclipse - Install the dev-util/eclipse-sdk plugins
 dev-lang/julia:int64 - Build with 64 bits integer blas and lapack (needs sci-libs/openblas and sci-libs/lapack-reference)
 dev-lang/path64:assembler - Build PathAS assembler
 dev-lang/path64:debugger - Build PathDB debugger
@@ -32,6 +34,7 @@ dev-lang/path64:valgrind - Support compiler debugging with dev-util/valgrind
 dev-lang/pgi:acml - Install AMD's core math library.
 dev-lang/pgi:cuda - Install PGI's CUDA components (e.g. for OpenACC)
 dev-lang/pgi:java - Install a PGI-tuned JRE.
+dev-libs/intel-common:compiler - Install the libraries needed for the icc and ifort compilers
 dev-libs/libflatarray:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator)
 dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
 dev-ml/zarith:mpir - Use sci-libs/mpir for arbitrary precision integer arithmetic

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

[Justin Lecher]

commit:     36429cadd4aac62f5fc96edfbb830830bfa39397
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan  6 11:36:59 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan  6 11:37:11 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=36429cad

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index e64fe6d..3a63e67 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -73,7 +73,6 @@ sci-biology/ncbi-blast+:freetype - Undocumented USE
 sci-biology/ncbi-blast+:mesa - Undocumented USE
 sci-biology/ncbi-blast+:muparser - Undocumented USE
 sci-biology/ncbi-blast+:sablotron - Undocumented USE
-sci-biology/ncbi-blast+:sqlite3 - Add support for dev-db/sqlite:3
 sci-biology/ncbi-blast+:xalan - Undocumented USE
 sci-biology/ncbi-blast+:xerces - Undocumented USE
 sci-biology/ncbi-blast+:xslt - Undocumented USE
@@ -83,7 +82,6 @@ sci-biology/ncbi-tools++:freetype - Undocumented USE
 sci-biology/ncbi-tools++:mesa - Undocumented USE
 sci-biology/ncbi-tools++:muparser - Undocumented USE
 sci-biology/ncbi-tools++:sablotron - Undocumented USE
-sci-biology/ncbi-tools++:sqlite3 - Add support for dev-db/sqlite:3
 sci-biology/ncbi-tools++:xalan - Undocumented USE
 sci-biology/ncbi-tools++:xerces - Undocumented USE
 sci-biology/ncbi-tools++:xslt - Undocumented USE
@@ -208,6 +206,7 @@ sci-libs/itk:vtkglue - PLEASE FIX MY DESCRIPTION
 sci-libs/lapack-reference:deprecated - Build deprecated routines
 sci-libs/lapack-reference:int64 - Build the 64 bits integer library
 sci-libs/lapack-reference:xblas - Build LAPACK with extra precision (needs sci-libs/xblas)
+sci-libs/lapacke-reference:deprecated - Build deprecated routines
 sci-libs/lapacke-reference:tmg - Build LAPACKE with a Test Matrix Generator library
 sci-libs/lapacke-reference:xblas - Build LAPACKE with extra precision (needs sci-libs/xblas)
 sci-libs/libfac:singular - Automatically generated description for singular

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

[Justin Lecher]

commit:     435a2eea5897268889a2b931a1f134c56fe1d758
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 11 12:00:09 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 11 12:00:09 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=435a2eea

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 3a63e67..6d7e6e2 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -220,14 +220,12 @@ sci-libs/libgeodecomp:visit - Add in situ visualization for big simulations via
 sci-libs/libsc:romio - Build with support for the ROMIO MPI-IO component
 sci-libs/lwpr:octave - Add sci-mathematics/octave support
 sci-libs/mkl:int64 - Build the 64 bits integer library
-sci-libs/nexus:cbf - Support for Crystallographic Binary Format files with sci-libs/cbflib
 sci-libs/nexus:doc - Generate library documentation with app-doc/doxygen
 sci-libs/nexus:fortran - Build the Fortran bindings
-sci-libs/nexus:guile - Build the Scheme bindings
+sci-libs/nexus:hdf4 - Support the old HDF4 representation
+sci-libs/nexus:hdf5 - Support the standard representation (HDF5)
 sci-libs/nexus:java - Build the Java bindings
-sci-libs/nexus:python - Build the Python bindings
-sci-libs/nexus:swig - Generate bindings with dev-lang/swig
-sci-libs/nexus:tcl - Build the TCL bindings
+sci-libs/nexus:utils - Build optional utility applications
 sci-libs/nexus:xml - Allow using the verbose XML representation of NeXus data
 sci-libs/nibabel:dicom - Adds limited read support for the DICOM imaging format.
 sci-libs/oasa:cairo - Add support for Cairo graphics library using dev-python/pycairo

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

[Justin Lecher]

commit:     176017694a2ed061a6660483b910beba39792021
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 14 09:54:47 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 14 09:54:47 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=17601769

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 6d7e6e2..d288de8 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -125,6 +125,7 @@ sci-chemistry/rosetta:lange - Apply patches from www.csrosetta.org
 sci-chemistry/shiftx2:debug - Enables debug output in the shiftx2 java part
 sci-chemistry/votca-csg:extras - Pull in extra applications from sci-chemistry/votca-csg-apps
 sci-chemistry/votca-csg:gromacs - Add support for gromacs file formats through sci-chemistry/gromacs
+sci-chemistry/wxmacmolplt:flash - Add support for flash movie generation using media-libs/ming
 sci-electronics/player:boost - Automatically generated description for boost
 sci-electronics/player:festival - Automatically generated description for festival
 sci-electronics/player:openssl - Automatically generated description for openssl

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

[Justin Lecher]

commit:     7d683179f177151fe4d0ecd8dda4c2218ba38299
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Feb  9 13:26:48 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Feb  9 13:26:48 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d683179

Mask sci-biology/inGAP-bin because sci-biology/biojava is gone

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index b67f4fc..54af1f6 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher <jlec@gentoo.org> (9 Feb 2016)
+# rev dep masked
+sci-biology/inGAP-bin
+
 # Andreas K. Huettel <dilfridge@gentoo.org> (1 Nov 2014)
 # Lab::Instrument and Lab::Tools provided as separate packages
 # are way outdated. These are now supplied as parts of the package

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

[Justin Lecher]

commit:     c5877a5eed847e2ab76d77697b3783e05236f14a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 11 07:58:35 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Feb 11 07:58:35 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c5877a5e

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index d288de8..2d940d1 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -40,7 +40,6 @@ dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
 dev-ml/zarith:mpir - Use sci-libs/mpir for arbitrary precision integer arithmetic
 dev-python/ffnet:matplotlib - Use matplotlib for drawing
 dev-python/pyhdf:szip - Allow to use sci-libs/szip for SZIP compression method in SDsetcompress()
-dev-python/ufl:scipy - Adds support for evaluating Bessel functions using dev-python/scipy
 dev-tex/pythontex:highlighting - PLEASE FIX MY DESCRIPTION
 dev-util/VampirTrace:cuda - Enable tracing of CUDA calls and GPU kernels.
 dev-util/amdapp:examples - Build the OpenCL example programs

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

[Justin Lecher]

commit:     77a503f0e2b7cbd2cf0acd4ec75f9b10fdb7ea3b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 12 09:26:12 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 12 09:26:12 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=77a503f0

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 2d940d1..92e1a4d 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -200,6 +200,7 @@ sci-libs/gmsh:tetgen - Enable 3D delauny triangulation using tetgen lib
 sci-libs/gotoblas2:incblas - Build the CBLAS interface
 sci-libs/gotoblas2:int64 - Build the 64 bits integer library
 sci-libs/gsl:cblas-external - Link gsl with external cblas provided by (virtual/cblas) instead of shipped internal version
+sci-libs/gsl:int64 - Build the 64 bits integer library
 sci-libs/itk:itkv3compat - Enable compatibility with ITK version 3
 sci-libs/itk:review - Enable compilation of methods under review
 sci-libs/itk:vtkglue - PLEASE FIX MY DESCRIPTION

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

[Justin Lecher]

commit:     23da5c7c7dab32895fef12695bf2daf8f9167661
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 19 09:27:13 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 19 09:27:13 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=23da5c7c

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 92e1a4d..df3b043 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -24,7 +24,6 @@ dev-lang/berkeley_upc:sptr-struct - Use the 'struct' shared pointer representati
 dev-lang/berkeley_upc:sptr-symmetric - Enable 'symmetric' pointer variant where available (64-bit smp and shmem)
 dev-lang/berkeley_upc:udp - Support running over UDP
 dev-lang/conceptual:gui - Build the Java base graphical interface
-dev-lang/icc:eclipse - Install the dev-util/eclipse-sdk plugins
 dev-lang/idb:eclipse - Install the dev-util/eclipse-sdk plugins
 dev-lang/julia:int64 - Build with 64 bits integer blas and lapack (needs sci-libs/openblas and sci-libs/lapack-reference)
 dev-lang/path64:assembler - Build PathAS assembler
@@ -35,6 +34,7 @@ dev-lang/pgi:acml - Install AMD's core math library.
 dev-lang/pgi:cuda - Install PGI's CUDA components (e.g. for OpenACC)
 dev-lang/pgi:java - Install a PGI-tuned JRE.
 dev-libs/intel-common:compiler - Install the libraries needed for the icc and ifort compilers
+dev-libs/intel-common:mic - Install the libraries needed for supporting Intel Many Integrated Core (Xeon Phi)
 dev-libs/libflatarray:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator)
 dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
 dev-ml/zarith:mpir - Use sci-libs/mpir for arbitrary precision integer arithmetic
@@ -221,6 +221,7 @@ sci-libs/libgeodecomp:visit - Add in situ visualization for big simulations via
 sci-libs/libsc:romio - Build with support for the ROMIO MPI-IO component
 sci-libs/lwpr:octave - Add sci-mathematics/octave support
 sci-libs/mkl:int64 - Build the 64 bits integer library
+sci-libs/mkl:mic - Install the libraries needed for supporting Intel Many Integrated Core (Xeon Phi)
 sci-libs/nexus:doc - Generate library documentation with app-doc/doxygen
 sci-libs/nexus:fortran - Build the Fortran bindings
 sci-libs/nexus:hdf4 - Support the old HDF4 representation

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

[Justin Lecher]

commit:     88b62329f55c3a8ee9ddb03418f4d293ac243f7a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 22 10:58:44 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 22 10:58:44 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=88b62329

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index df3b043..539b98b 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -239,8 +239,6 @@ sci-libs/pagmo:kepler - Automatically generated description for kepler
 sci-libs/pagmo:nlopt - Automatically generated description for nlopt
 sci-libs/parmetis:double-precision - Floating-point operation done as double precision
 sci-libs/parmetis:int64 - Build the 64 bits integer library (needed for > 2^31 vertices)
-sci-libs/pastix:int64 - Build the 64 bits integer library
-sci-libs/pastix:starpu - Build and link with dev-libs/starpu
 sci-libs/scikits_image:freeimage - Enable support for image i/o via media-libs/freeimage
 sci-libs/scikits_image:pyamg - Enable support for algebraic solvers via dev-python/pyamg
 sci-libs/symengine:boost - Add support for boost (dev-libs/boost)

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

[Justin Lecher]

commit:     5b74250f256b4fb0b5bfe2cab6de1431e8b400fb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 29 17:20:55 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 29 17:20:55 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5b74250f

profiles: Mask sci-biology/perlprimer due to unknown revdep

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 54af1f6..da52aee 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher <jlec@gentoo.org> (29 Feb 2016)
+# unknown rev dep masked
+sci-biology/perlprimer
+
 # Justin Lecher <jlec@gentoo.org> (9 Feb 2016)
 # rev dep masked
 sci-biology/inGAP-bin

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

[Justin Lecher]

commit:     457e338226b47ef19c891d8519cf5edbb09aeec6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 24 07:27:13 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 24 07:27:13 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=457e3382

Mask sci-biology/genseed due to missing rev dep

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 54af1f6..765c3b2 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Justin Lecher <jlec@gentoo.org> (24 April 2016)
+# rev dep absent
+sci-biology/genseed
+
 # Justin Lecher <jlec@gentoo.org> (9 Feb 2016)
 # rev dep masked
 sci-biology/inGAP-bin

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

[Justin Lecher]

commit:     78b4d397a13876142e0ab46f9cd34f6ea7e3d32c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 24 07:29:41 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 24 07:29:41 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=78b4d397

Mask packages with missing rev dep KEYWORDS

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 765c3b2..4bac753 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,6 +34,10 @@
 # rev dep absent
 sci-biology/genseed
 
+# Justin Lecher <jlec@gentoo.org> (24 April 2016)
+# rev dep missing keywords
+sci-biology/iCORN2
+
 # Justin Lecher <jlec@gentoo.org> (9 Feb 2016)
 # rev dep masked
 sci-biology/inGAP-bin

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

[Justin Lecher]

commit:     ccccc89995ccec5a9ff82fd13e711ad064a63fa4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 24 07:38:22 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 24 07:38:22 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ccccc899

Mask sci-biology/tgicl because of broken deptree

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/package.mask | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 4bac753..3ceaf54 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,6 +33,7 @@
 # Justin Lecher <jlec@gentoo.org> (24 April 2016)
 # rev dep absent
 sci-biology/genseed
+sci-biology/tgicl
 
 # Justin Lecher <jlec@gentoo.org> (24 April 2016)
 # rev dep missing keywords

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

[Justin Lecher]

commit:     7cce2dc28fd9be215977716245ce708fe3cfdd92
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 24 07:49:59 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 24 07:49:59 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7cce2dc2

Mask sci-mathematics/scilab due to broken dep tree

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/package.mask | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3ceaf54..8a647df 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,6 +34,7 @@
 # rev dep absent
 sci-biology/genseed
 sci-biology/tgicl
+sci-mathematics/scilab
 
 # Justin Lecher <jlec@gentoo.org> (24 April 2016)
 # rev dep missing keywords

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

[Justin Lecher]

commit:     f1718b937ac113f920e8649e8fb883ed87f0f9d2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 26 19:06:20 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr 26 19:06:20 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1718b93

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 539b98b..e3ba980 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -49,7 +49,6 @@ dev-util/nvidia-cuda-gdk:nvvs - Install the NVIDIA Validation Suite.
 media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled)
 media-gfx/librecad:3d - Require all 2D coordinates stored as 3D
 media-gfx/librecad:tools - Build additional tool programs: tff2lff
-sci-astronomy/astrometry:extra - Add extra tools, specifically for plots
 sci-astronomy/mosstack:opencl - Enables OpenCL support and pulls in pyopencl. This makes some operations much faster but requires specific hardware and drivers.
 sci-astronomy/mosstack:qt4 - Pulls in PyQt4. Program works on command line interface without it but for GUI the library is required.
 sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
@@ -246,17 +245,17 @@ sci-libs/trilinos:adolc - Add support for adolc (sci-libs/adolc)
 sci-libs/trilinos:arprec - Add support for arprec (sci-libs/arprec)
 sci-libs/trilinos:boost - Add support for boost (dev-libs/boost)
 sci-libs/trilinos:clp - Add support for clp (sci-libs/coinor-clp)
-sci-libs/trilinos:cppunit - Add support for ()
+sci-libs/trilinos:cppunit - Add support for (...)
 sci-libs/trilinos:cuda - Add support for cuda (dev-util/nvidia-cuda-toolkit)
 sci-libs/trilinos:eigen - Add support for eigen (dev-cpp/eigen)
-sci-libs/trilinos:glpk - Add support for ()
+sci-libs/trilinos:glpk - Add support for (...)
 sci-libs/trilinos:gtest - Add support for gtest (dev-cpp/gtest)
 sci-libs/trilinos:hdf5 - Add support for hdf5 (sci-libs/hdf5)
 sci-libs/trilinos:hwloc - Add support for hwloc (sys-apps/hwloc)
 sci-libs/trilinos:hypre - Add support for hypre (sci-libs/hypre)
 sci-libs/trilinos:matio - Add support for matio (sci-libs/matio)
-sci-libs/trilinos:metis - Add support for metis (sci-libs/(par)metis)
-sci-libs/trilinos:mkl - Add support for mkl (sci/libs/mkl)
+sci-libs/trilinos:metis - Add support for metis (sci-libs/metis or sci-libs/parmetis)
+sci-libs/trilinos:mkl - Add support for mkl (sci-libs/mkl)
 sci-libs/trilinos:mumps - Add support for mumps (sci-libs/mumps)
 sci-libs/trilinos:netcdf - Add support for netcdf (sci-libs/netcdf)
 sci-libs/trilinos:petsc - Add support for petsc (sci-mathematics/petsc)
@@ -268,7 +267,7 @@ sci-libs/trilinos:superlu - Add support for superlu (sci-libs/superlu)
 sci-libs/trilinos:taucs - Add support for taucs (sci-libs/taucs)
 sci-libs/trilinos:tbb - Add support for threading building blocks library (dev-cpp/tbb)
 sci-libs/trilinos:tvmet - Add support for tvmet (dev-libs/tvmet)
-sci-libs/trilinos:yaml - Add support for yaml (dev-cpp-yaml)
+sci-libs/trilinos:yaml - Add support for yaml (dev-cpp/yaml)
 sci-libs/xblas:int64 - Build the 64 bits integer library
 sci-mathematics/Macaulay2:optimization - Disable to build with -O0 for debugging.
 sci-mathematics/acl2:books - build community books, the canonical collection of open-source libraries

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

[Christoph Junghans]

commit:     ea368df77e7a7aa6a2f4edeec7b20ead2837e3d7
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon May 30 20:58:32 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon May 30 20:58:32 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea368df7

Update local USE description

 profiles/use.local.desc | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index e3ba980..1c2c8bc 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -46,6 +46,11 @@ dev-util/amdapp:examples - Build the OpenCL example programs
 dev-util/nvidia-cuda-gdk:healthmon - Install nvidia-healthmon.
 dev-util/nvidia-cuda-gdk:nvml - Install the NVIDIA Managment Library.
 dev-util/nvidia-cuda-gdk:nvvs - Install the NVIDIA Validation Suite.
+dev-util/nvidia-cuda-sdk:cuda - Build CUDA binaries.
+dev-util/nvidia-cuda-sdk:opencl - Build OpenCL binaries.
+dev-util/nvidia-cuda-toolkit:debugger - Installs the CUDA debugger.
+dev-util/nvidia-cuda-toolkit:eclipse - Install plugins for eclipse
+dev-util/nvidia-cuda-toolkit:profiler - Installs the NVIDIA CUDA visual profiler.
 media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled)
 media-gfx/librecad:3d - Require all 2D coordinates stored as 3D
 media-gfx/librecad:tools - Build additional tool programs: tff2lff
@@ -268,6 +273,20 @@ sci-libs/trilinos:taucs - Add support for taucs (sci-libs/taucs)
 sci-libs/trilinos:tbb - Add support for threading building blocks library (dev-cpp/tbb)
 sci-libs/trilinos:tvmet - Add support for tvmet (dev-libs/tvmet)
 sci-libs/trilinos:yaml - Add support for yaml (dev-cpp/yaml)
+sci-libs/vtk:R - Enable support for dev-lang/R
+sci-libs/vtk:all-modules - Build all modules
+sci-libs/vtk:boost - Add support for boost
+sci-libs/vtk:cg - Use nvidia's cg shaders
+sci-libs/vtk:gdal - Support for gdal formated data
+sci-libs/vtk:imaging - Building Imaging modules
+sci-libs/vtk:json - Support for json formated data
+sci-libs/vtk:kaapi - Use sci-libs/xkaapi to handle smp support
+sci-libs/vtk:offscreen - Offscreen rendering through OSMesa
+sci-libs/vtk:rendering - Building Redering modules
+sci-libs/vtk:tbb - Use dev-cpp/tbb to handle smp support
+sci-libs/vtk:views - Building Views modules
+sci-libs/vtk:web - Install web component
+sci-libs/vtk:xdmf2 - Support for xdmf2 formated data
 sci-libs/xblas:int64 - Build the 64 bits integer library
 sci-mathematics/Macaulay2:optimization - Disable to build with -O0 for debugging.
 sci-mathematics/acl2:books - build community books, the canonical collection of open-source libraries

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

[Andrew Savchenko]

commit:     5ded8e6a0e7f46a3e6e9cef991f03d4a25c563e5
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Thu Jun  2 17:47:09 2016 +0000
Commit:     Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
CommitDate: Thu Jun  2 17:47:09 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5ded8e6a

Mask sci-physics/qcl plotutils

qcl is long broken to plotutils, so mask it until fixed (looks like
a problem in libplotter->libxmi linking), needs further
investigation.

 profiles/package.use.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index f66f9b2..1b6e427 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -16,6 +16,10 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
+# Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
+# doesn't link with plotutils-2.6
+sci-physics/qcl plotutils
+
 # Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014)
 # icc and ifc don't work on no-multilib
 sci-biology/estscan icc ifc

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

[Christoph Junghans]

commit:     f58159e1d2bd4abbea2b42cf3f4bebfc5d3f40f6
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 22 19:21:48 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jul 22 19:21:48 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f58159e1

Update local USE description

 profiles/use.local.desc | 30 ++----------------------------
 1 file changed, 2 insertions(+), 28 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 1c2c8bc..e12d73d 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -37,7 +37,6 @@ dev-libs/intel-common:compiler - Install the libraries needed for the icc and if
 dev-libs/intel-common:mic - Install the libraries needed for supporting Intel Many Integrated Core (Xeon Phi)
 dev-libs/libflatarray:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator)
 dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
-dev-ml/zarith:mpir - Use sci-libs/mpir for arbitrary precision integer arithmetic
 dev-python/ffnet:matplotlib - Use matplotlib for drawing
 dev-python/pyhdf:szip - Allow to use sci-libs/szip for SZIP compression method in SDsetcompress()
 dev-tex/pythontex:highlighting - PLEASE FIX MY DESCRIPTION
@@ -60,6 +59,7 @@ sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plot
 sci-astronomy/scamp:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
 sci-astronomy/sextractor:modelfit - Enable profile model fitting, needs sci-libs/atlas and sci-libs/fftw
 sci-astronomy/zpeg:gdl - Install GDL/IDL plotting routines
+sci-biology/abyss:misc-haskell - build abyss-samtobreak tool, pull in haskell toolchain
 sci-biology/bru2nii:gui - Build graphical user interface
 sci-biology/discrover:cairo - Use Cairo for sequence logo plotting capabilities
 sci-biology/discrover:dreme - Enable usage of DREME from the MEME package for seeding
@@ -69,7 +69,6 @@ sci-biology/discrover:rmathlib - Link to the standalone Rmathlib for statistical
 sci-biology/estscan:icc - Undocumented USE
 sci-biology/estscan:ifc - Undocumented USE
 sci-biology/exonerate-gff3:utils - Unknown
-sci-biology/hmmer:pvm - Add support for parallel virtual machine (sys-cluster/pvm)
 sci-biology/ncbi-blast+:boost - Undocumented USE
 sci-biology/ncbi-blast+:cppunit - Undocumented USE
 sci-biology/ncbi-blast+:freetype - Undocumented USE
@@ -97,14 +96,6 @@ sci-chemistry/gamess:neo - Enable NEO for nuclear basis support
 sci-chemistry/gamess:pax_kernel - Make this package work on PAX kernels
 sci-chemistry/gamess:qmmm-tinker - Enable tinker qmmm code
 sci-chemistry/gnome-chemistry-utils:gnumeric - Build pluging for gnumeric
-sci-chemistry/gromacs:boost - Enable external boost library
-sci-chemistry/gromacs:cuda - Enable cuda non-bonded kernels
-sci-chemistry/gromacs:double-precision - More precise calculations at the expense of speed
-sci-chemistry/gromacs:make-symlinks - Create symbolic links for pre-5.0 binary names
-sci-chemistry/gromacs:mkl - Use sci-libs/mkl for fft, blas, lapack routines
-sci-chemistry/gromacs:offensive - Enable gromacs partly offensive quotes
-sci-chemistry/gromacs:single-precision - Single precision version of gromacs (default)
-sci-chemistry/gromacs:tng - Enable new trajectory format - tng
 sci-chemistry/mdsctk:R - Install dev-lang/R scripts as well
 sci-chemistry/nwchem:blas - Use external BLAS library instead of the internal routines
 sci-chemistry/nwchem:cuda - Enable CUDA GPU support for the Tensor Contraction Engine generated methods (CI, MBPT, CC)
@@ -126,8 +117,6 @@ sci-chemistry/rosetta:boost - compile rosetta with boost supported code
 sci-chemistry/rosetta:float - Build with floats rather than doubles
 sci-chemistry/rosetta:lange - Apply patches from www.csrosetta.org
 sci-chemistry/shiftx2:debug - Enables debug output in the shiftx2 java part
-sci-chemistry/votca-csg:extras - Pull in extra applications from sci-chemistry/votca-csg-apps
-sci-chemistry/votca-csg:gromacs - Add support for gromacs file formats through sci-chemistry/gromacs
 sci-chemistry/wxmacmolplt:flash - Add support for flash movie generation using media-libs/ming
 sci-electronics/player:boost - Automatically generated description for boost
 sci-electronics/player:festival - Automatically generated description for festival
@@ -184,8 +173,6 @@ sci-libs/dealii:tbb - Add threading support with the help of the tbb library (de
 sci-libs/dealii:trilinos - Add support for trilinos (sci-libs/trilinos)
 sci-libs/etsf_io:pic - Compile Position Independent Code
 sci-libs/factory:singular - Enable support for sci-mathematics/singular
-sci-libs/fftw:quad - Build quadruple precision lib
-sci-libs/fftw:zbus - Adds support for ZBus cycle-counter of mips
 sci-libs/fox:dom - Compile the W3C document object model module
 sci-libs/fox:fast - Compile with best known optimization flags
 sci-libs/fox:sax - Compile the streaming, validating parser based on java's Simple API for XML
@@ -361,16 +348,12 @@ sci-physics/bigdft:scalapack - Use ScaLAPACK, a subset of LAPACK routines redesi
 sci-physics/elk:libxc - Use sci-libs/libxc library of exchange-correlation functionals by ETSF.
 sci-physics/elk:perl - Install perl scripts.
 sci-physics/elk:python - Install python scripts.
-sci-physics/espresso:cuda - Enable cuda support
-sci-physics/espresso:examples - Installs the examples
-sci-physics/espresso:packages - Installs extra subpackages
 sci-physics/geant-vmc:g4root - Build G4Root (interface for GEANT4 simulation with a ROOT geometry)
 sci-physics/geant-vmc:geant3 - Build with Geant4 G3toG4 library
 sci-physics/geant-vmc:mtroot - Build MTRoot (provides ROOT IO manager classes with multi-threading support)
 sci-physics/geant-vmc:vgm - Enable the Virtual Geometry Model (sci-physics/vgm)
 sci-physics/herwig++:c++11 - Build Herwig++ using the C++11 standard. Experimental feature, not for production use.
 sci-physics/herwig++:fastjet - Adds support for sci-physics/fastjet
-sci-physics/hoomd-blue:cuda - Enable cuda non-bonded kernels
 sci-physics/mc-tester:hepmc - Compile sci-physics/hepmc interface
 sci-physics/root:fits - Support for images and data from FITS files with sci-libs/cfitsio
 sci-physics/root:geocad - Enable ROOT-CAD interface using sci-libs/opencascade
@@ -384,10 +367,6 @@ sci-physics/tauola:tau-spinner - Compile with TauSpinner library
 sci-physics/vgm:geant4 - Enable interaction with Geant4(sci-physics/geant:4)
 sci-physics/vgm:root - Enable interactions with ROOT (sci-physics/root)
 sci-physics/yoda:root - Adds support for sci-physics/root
-sci-visualization/gnuplot:bitmap - Enable dot-matrix printers and pbm terminal
-sci-visualization/gnuplot:compat - Enable backwards compatibility with version 4 syntax
-sci-visualization/gnuplot:gd - Add support for media-libs/gd. Needed for GIF, JPEG, and PNG image output.
-sci-visualization/gnuplot:libcerf - Enable special functions from sci-libs/libcerf
 sci-visualization/mantid:doc - Generate documentation with app-doc/doxygen, QT Assistant etc
 sci-visualization/mantid:opencascade - Use OpenCascade to show 3D models of instruments
 sci-visualization/mantid:opencl - Use OpenCL to accelerate calculations
@@ -398,10 +377,6 @@ sci-visualization/v_sim:abinit - Add support for ABINIT file formats sci-physics
 sci-visualization/v_sim:cube - Add support plug-in support for Cube files (densities and structures)
 sci-visualization/v_sim:openbabel - Add support for ABINIT file formats sci-chemistry/openbabel
 sci-visualization/v_sim:xsf - plug-in support for files that follow the XCrysDen format for structural positions and densities
-sys-cluster/hpx:jemalloc - Use dev-libs/jemalloc for memory allocation
-sys-cluster/hpx:papi - Use dev-libs/papi for NaCl
-sys-cluster/hpx:perftools - Use dev-util/google-perftools for memory allocation
-sys-cluster/hpx:tbb - Use dev-cpp/tbb for memory allocation
 sys-cluster/htcondor:X - Enable the HTCondor Keyboard Daemon to monitor logged in X users for activity
 sys-cluster/htcondor:boinc - Enable backfill with BOINC jobs when the cluster is not being used
 sys-cluster/htcondor:cgroup - Use dev-libs/libcgroup for kernel control groups
@@ -411,10 +386,9 @@ sys-cluster/htcondor:libvirt - Use app-emulation/libvirt for virtualisation
 sys-cluster/htcondor:management - Use net-libs/qmf for management
 sys-cluster/htcondor:minimal - Don't support standard universe jobs
 sys-cluster/lustre:client - Enable kernel client modules
-sys-cluster/lustre:liblustre - Enable building of liblustre
+sys-cluster/lustre:dlc - Enable Dynamic LNET Configuration
 sys-cluster/lustre:server - Enable kernels server modules
 sys-cluster/lustre:tests - Enable installation of tests
-sys-cluster/lustre:urandom - Enable use of urandom
 sys-cluster/lustre:utils - Enable lustre utils
 sys-cluster/mpich:mpi-threads - Enable MPI_THREAD_MULTIPLE
 sys-cluster/mpich:romio - Build the ROMIO MPI-IO component

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

[Christoph Junghans]

commit:     6afbffb9dba46246b10c42abd65e6894608c17fd
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Sep  5 23:59:02 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Sep  5 23:59:02 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6afbffb9

package.mask: mask virtual mpi

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 8a647df..481e78d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Christoph Junghans <ottxor@gentoo.org> (05 Sep 2016)
+# use the one from gx86 instead
+virtual/mpi
+
 # Justin Lecher <jlec@gentoo.org> (24 April 2016)
 # rev dep absent
 sci-biology/genseed

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

[Christoph Junghans]

commit:     64796d9e2681b8c11377ce980a4ae686646031be
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 21 01:26:21 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Sep 21 01:26:21 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=64796d9e

profiles: drop old mask

 profiles/package.mask   | 4 ----
 profiles/use.local.desc | 1 -
 2 files changed, 5 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 481e78d..8a647df 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,10 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Christoph Junghans <ottxor@gentoo.org> (05 Sep 2016)
-# use the one from gx86 instead
-virtual/mpi
-
 # Justin Lecher <jlec@gentoo.org> (24 April 2016)
 # rev dep absent
 sci-biology/genseed

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index e12d73d..5e56627 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -409,6 +409,5 @@ virtual/blas:int64 - Add eselect module for blas libraries built with 64 bits in
 virtual/cblas:int64 - Add eselect module for cblas libraries built with 64 bits integer ABI
 virtual/lapack:int64 - Add eselect module for lapack libraries built with 64 bits integer ABI
 virtual/lapacke:int64 - Add eselect module for blas libraries built with 64 bits integer ABI
-virtual/mpi:romio - Enable romio, a high-performance portable MPI-IO
 virtual/scalapack:int64 - Add eselect module for blas libraries built with 64 bits integer ABI
 x11-libs/agg:gpc - Enable gpc polygon clipper library

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

[Justin Lecher]

commit:     5866eaa2d3c423c979854582058d99c808d78991
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 28 13:45:39 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Oct 28 13:45:39 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5866eaa2

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 5e56627..9101a77 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -25,7 +25,6 @@ dev-lang/berkeley_upc:sptr-symmetric - Enable 'symmetric' pointer variant where
 dev-lang/berkeley_upc:udp - Support running over UDP
 dev-lang/conceptual:gui - Build the Java base graphical interface
 dev-lang/idb:eclipse - Install the dev-util/eclipse-sdk plugins
-dev-lang/julia:int64 - Build with 64 bits integer blas and lapack (needs sci-libs/openblas and sci-libs/lapack-reference)
 dev-lang/path64:assembler - Build PathAS assembler
 dev-lang/path64:debugger - Build PathDB debugger
 dev-lang/path64:native - Use EKOPath/Path64 for bootstraping
@@ -53,6 +52,9 @@ dev-util/nvidia-cuda-toolkit:profiler - Installs the NVIDIA CUDA visual profiler
 media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled)
 media-gfx/librecad:3d - Require all 2D coordinates stored as 3D
 media-gfx/librecad:tools - Build additional tool programs: tff2lff
+net-misc/cernbox-client:dolphin - Install the kde-apps/dolphin extension
+net-misc/cernbox-client:nautilus - Install the gnome-base/nautilus extension
+net-misc/cernbox-client:sftp - Enable sftp transfer support via net-libs/libssh
 sci-astronomy/mosstack:opencl - Enables OpenCL support and pulls in pyopencl. This makes some operations much faster but requires specific hardware and drivers.
 sci-astronomy/mosstack:qt4 - Pulls in PyQt4. Program works on command line interface without it but for GUI the library is required.
 sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing

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

[Justin Lecher]

commit:     edf11b310b1b7b3ccbe53eeadea74b808ee40e41
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 30 18:33:38 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Oct 30 18:33:38 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=edf11b31

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 9101a77..0685998 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -44,11 +44,6 @@ dev-util/amdapp:examples - Build the OpenCL example programs
 dev-util/nvidia-cuda-gdk:healthmon - Install nvidia-healthmon.
 dev-util/nvidia-cuda-gdk:nvml - Install the NVIDIA Managment Library.
 dev-util/nvidia-cuda-gdk:nvvs - Install the NVIDIA Validation Suite.
-dev-util/nvidia-cuda-sdk:cuda - Build CUDA binaries.
-dev-util/nvidia-cuda-sdk:opencl - Build OpenCL binaries.
-dev-util/nvidia-cuda-toolkit:debugger - Installs the CUDA debugger.
-dev-util/nvidia-cuda-toolkit:eclipse - Install plugins for eclipse
-dev-util/nvidia-cuda-toolkit:profiler - Installs the NVIDIA CUDA visual profiler.
 media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled)
 media-gfx/librecad:3d - Require all 2D coordinates stored as 3D
 media-gfx/librecad:tools - Build additional tool programs: tff2lff

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

[Justin Lecher]

commit:     10dc39c988e5a171cda9b61de822a5b7a29e00a7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 26 11:09:42 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov 26 11:09:42 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=10dc39c9

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 16 +---------------
 1 file changed, 1 insertion(+), 15 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 0685998..0f2c81b 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -136,7 +136,7 @@ sci-libs/arrayfire:graphics - Build with Forge graphics.
 sci-libs/arrayfire:nonfree - Build ArrayFire nonfree algorithms.
 sci-libs/arrayfire:opencl - Build OpenCL backend.
 sci-libs/arrayfire:unified - Build Backend-Independent API.
-sci-libs/asl:matio - Matlab support with sci-libs/matio
+sci-libs/asl:matlab - Matlab support with sci-libs/matio
 sci-libs/atlas:deprecated - Build deprecated routines
 sci-libs/atlas:generic - Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)
 sci-libs/atlas:ifko - Use iFKO to improve ATLAS performance (ATTENTION!!! Increases builtime enormously)
@@ -257,20 +257,6 @@ sci-libs/trilinos:taucs - Add support for taucs (sci-libs/taucs)
 sci-libs/trilinos:tbb - Add support for threading building blocks library (dev-cpp/tbb)
 sci-libs/trilinos:tvmet - Add support for tvmet (dev-libs/tvmet)
 sci-libs/trilinos:yaml - Add support for yaml (dev-cpp/yaml)
-sci-libs/vtk:R - Enable support for dev-lang/R
-sci-libs/vtk:all-modules - Build all modules
-sci-libs/vtk:boost - Add support for boost
-sci-libs/vtk:cg - Use nvidia's cg shaders
-sci-libs/vtk:gdal - Support for gdal formated data
-sci-libs/vtk:imaging - Building Imaging modules
-sci-libs/vtk:json - Support for json formated data
-sci-libs/vtk:kaapi - Use sci-libs/xkaapi to handle smp support
-sci-libs/vtk:offscreen - Offscreen rendering through OSMesa
-sci-libs/vtk:rendering - Building Redering modules
-sci-libs/vtk:tbb - Use dev-cpp/tbb to handle smp support
-sci-libs/vtk:views - Building Views modules
-sci-libs/vtk:web - Install web component
-sci-libs/vtk:xdmf2 - Support for xdmf2 formated data
 sci-libs/xblas:int64 - Build the 64 bits integer library
 sci-mathematics/Macaulay2:optimization - Disable to build with -O0 for debugging.
 sci-mathematics/acl2:books - build community books, the canonical collection of open-source libraries

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

[Justin Lecher]

commit:     3ff43126ef08c68830f29801ba69147f0f3136a3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan  4 10:34:19 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan  4 10:34:19 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3ff43126

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 0f2c81b..c03aafc 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -37,6 +37,7 @@ dev-libs/intel-common:mic - Install the libraries needed for supporting Intel Ma
 dev-libs/libflatarray:cuda - Enables plugins for NVIDIA GPUs (e.g. CUDAAllocator)
 dev-ml/mlgmpidl:mpfr - Add support for dev-libs/mpfr
 dev-python/ffnet:matplotlib - Use matplotlib for drawing
+dev-python/nbdime:webtools - Install web-based diff and merge tools.
 dev-python/pyhdf:szip - Allow to use sci-libs/szip for SZIP compression method in SDsetcompress()
 dev-tex/pythontex:highlighting - PLEASE FIX MY DESCRIPTION
 dev-util/VampirTrace:cuda - Enable tracing of CUDA calls and GPU kernels.
@@ -335,8 +336,6 @@ sci-physics/geant-vmc:g4root - Build G4Root (interface for GEANT4 simulation wit
 sci-physics/geant-vmc:geant3 - Build with Geant4 G3toG4 library
 sci-physics/geant-vmc:mtroot - Build MTRoot (provides ROOT IO manager classes with multi-threading support)
 sci-physics/geant-vmc:vgm - Enable the Virtual Geometry Model (sci-physics/vgm)
-sci-physics/herwig++:c++11 - Build Herwig++ using the C++11 standard. Experimental feature, not for production use.
-sci-physics/herwig++:fastjet - Adds support for sci-physics/fastjet
 sci-physics/mc-tester:hepmc - Compile sci-physics/hepmc interface
 sci-physics/root:fits - Support for images and data from FITS files with sci-libs/cfitsio
 sci-physics/root:geocad - Enable ROOT-CAD interface using sci-libs/opencascade
@@ -349,7 +348,6 @@ sci-physics/tauola:hepmc - Compile sci-physics/hepmc interface
 sci-physics/tauola:tau-spinner - Compile with TauSpinner library
 sci-physics/vgm:geant4 - Enable interaction with Geant4(sci-physics/geant:4)
 sci-physics/vgm:root - Enable interactions with ROOT (sci-physics/root)
-sci-physics/yoda:root - Adds support for sci-physics/root
 sci-visualization/mantid:doc - Generate documentation with app-doc/doxygen, QT Assistant etc
 sci-visualization/mantid:opencascade - Use OpenCascade to show 3D models of instruments
 sci-visualization/mantid:opencl - Use OpenCL to accelerate calculations

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

[Justin Lecher]

commit:     da05ac0ade861afbf4aa1281fe6e9a71e14faf7b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 12 19:07:33 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 12 19:07:33 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da05ac0a

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index c03aafc..fb2fae1 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -57,7 +57,6 @@ sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plot
 sci-astronomy/scamp:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing
 sci-astronomy/sextractor:modelfit - Enable profile model fitting, needs sci-libs/atlas and sci-libs/fftw
 sci-astronomy/zpeg:gdl - Install GDL/IDL plotting routines
-sci-biology/abyss:misc-haskell - build abyss-samtobreak tool, pull in haskell toolchain
 sci-biology/bru2nii:gui - Build graphical user interface
 sci-biology/discrover:cairo - Use Cairo for sequence logo plotting capabilities
 sci-biology/discrover:dreme - Enable usage of DREME from the MEME package for seeding

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

[Justin Lecher]

commit:     7e6bdf4a4e40c45f720b3abfce0477113a5ec4a6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb  1 19:32:32 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb  1 19:32:32 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7e6bdf4a

Import main arch.list

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/arch.list | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/profiles/arch.list b/profiles/arch.list
index db7b9fa..6b702f1 100644
--- a/profiles/arch.list
+++ b/profiles/arch.list
@@ -2,12 +2,15 @@ alpha
 amd64
 amd64-fbsd
 arm
+arm64
 hppa
 ia64
 m68k
 mips
+nios2
 ppc
 ppc64
+riscv
 s390
 sh
 sparc
@@ -17,28 +20,19 @@ x86-fbsd
 
 # Prefix keywords
 ppc-aix
-x86-freebsd
-x64-freebsd
-sparc64-freebsd
-hppa-hpux
-ia64-hpux
-x86-interix
 amd64-linux
 arm-linux
-ia64-linux
+arm64-linux
 ppc64-linux
 x86-linux
 ppc-macos
 x86-macos
 x64-macos
 m68k-mint
-x86-netbsd
-ppc-openbsd
-x86-openbsd
-x64-openbsd
 sparc-solaris
 sparc64-solaris
 x64-solaris
 x86-solaris
 x86-winnt
+x64-cygwin
 x86-cygwin

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

[Justin Lecher]

commit:     1aa53ff1632efb5f0f02350448d523239e14a1b2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 19:17:13 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 19:17:13 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1aa53ff1

Import CATs from gentoo.git

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/categories | 124 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 124 insertions(+)

diff --git a/profiles/categories b/profiles/categories
index c065c73da..3d47d6ca4 100644
--- a/profiles/categories
+++ b/profiles/categories
@@ -1,28 +1,124 @@
+app-accessibility
 app-admin
+app-antivirus
+app-arch
+app-backup
 app-benchmarks
+app-cdr
+app-crypt
+app-dicts
 app-doc
+app-editors
+app-emacs
+app-emulation
+app-eselect
 app-forensics
+app-i18n
+app-laptop
+app-leechcraft
+app-misc
+app-mobilephone
+app-office
+app-officeext
+app-pda
 app-portage
+app-shells
 app-text
 app-vim
+app-xemacs
+dev-ada
 dev-cpp
+dev-db
+dev-dotnet
+dev-embedded
+dev-erlang
+dev-games
+dev-go
+dev-haskell
 dev-java
 dev-lang
 dev-libs
+dev-lisp
+dev-lua
 dev-ml
 dev-perl
+dev-php
 dev-python
+dev-qt
+dev-ros
+dev-ruby
+dev-scheme
 dev-tcltk
 dev-tex
+dev-texlive
 dev-util
+dev-vcs
+games-action
+games-arcade
+games-board
+games-emulation
+games-engines
+games-fps
+games-kids
+games-misc
+games-mud
+games-puzzle
+games-roguelike
+games-rpg
+games-server
+games-simulation
+games-sports
+games-strategy
+games-util
+gnome-base
+gnome-extra
+gnustep-apps
+gnustep-base
+gnustep-libs
+java-virtuals
+kde-apps
+kde-frameworks
+kde-misc
+kde-plasma
+lxde-base
+lxqt-base
+mail-client
+mail-filter
+mail-mta
+mate-base
+mate-extra
+media-fonts
 media-gfx
 media-libs
+media-plugins
+media-radio
+media-sound
+media-tv
+media-video
+net-analyzer
+net-dialup
+net-dns
 net-firewall
+net-fs
 net-ftp
+net-im
+net-irc
+net-libs
+net-mail
 net-misc
+net-nds
+net-news
+net-nntp
+net-p2p
+net-print
+net-proxy
+net-voip
+net-wireless
 perl-core
+ros-meta
 sci-astronomy
 sci-biology
+sci-calculators
 sci-chemistry
 sci-electronics
 sci-geosciences
@@ -31,9 +127,37 @@ sci-mathematics
 sci-misc
 sci-physics
 sci-visualization
+sec-policy
+sys-apps
+sys-auth
+sys-block
+sys-boot
 sys-cluster
 sys-devel
 sys-fabric
+sys-firmware
+sys-freebsd
+sys-fs
+sys-kernel
+sys-libs
+sys-power
+sys-process
 virtual
+www-apache
+www-apps
+www-client
+www-misc
+www-plugins
+www-servers
+x11-apps
+x11-base
+x11-drivers
 x11-libs
 x11-misc
+x11-plugins
+x11-proto
+x11-terms
+x11-themes
+x11-wm
+xfce-base
+xfce-extra

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

[Justin Lecher]

commit:     40800c2b2a7c33488d96fdd4d4e2ded4f9235029
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 26 08:52:45 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 26 08:52:45 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=40800c2b

Drop more ancient CVS Header

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/package.use.mask | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 1b6e427f3..8f0e8c341 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -1,6 +1,5 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header$
 
 # When you add an entry to the top of this file, add your name, the date, and
 # an explanation of why something is getting masked. Please be extremely

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

[Justin Lecher]

commit:     314fb0842d0e75ac47645ad35177860a46bf1854
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 18 21:05:18 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 18 21:08:48 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=314fb084

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index fb2fae1ab..034de1a8c 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -267,6 +267,8 @@ sci-mathematics/dolfin:scotch - Adds support for graph partitioning with sci-lib
 sci-mathematics/dolfin:umfpack - Adds support for sparse solving with sci-libs/umfpack
 sci-mathematics/gambit:X - Enable gui support using wxWidgets.
 sci-mathematics/gap:xtom - Automatically generated description for xtom
+sci-mathematics/gismo:doc - Build doxygen-documentation
+sci-mathematics/gismo:examples - Build examples
 sci-mathematics/htk:hdecode - Install HDecode, a large vocabulary word recogniser
 sci-mathematics/htk:hlmtools - Install the tools for manipulation of language models
 sci-mathematics/htk:hslab - Install HSLab a label editor for speech label manipulation

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

[Justin Lecher]

commit:     6f4207de311b5a420522dd738d96a2b2d8576f69
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 21 19:18:45 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 21 19:18:48 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6f4207de

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 034de1a8c..f4769675b 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -66,6 +66,7 @@ sci-biology/discrover:rmathlib - Link to the standalone Rmathlib for statistical
 sci-biology/estscan:icc - Undocumented USE
 sci-biology/estscan:ifc - Undocumented USE
 sci-biology/exonerate-gff3:utils - Unknown
+sci-biology/imagej:plugins - Install additional plugins
 sci-biology/ncbi-blast+:boost - Undocumented USE
 sci-biology/ncbi-blast+:cppunit - Undocumented USE
 sci-biology/ncbi-blast+:freetype - Undocumented USE
@@ -188,7 +189,6 @@ sci-libs/gmsh:tetgen - Enable 3D delauny triangulation using tetgen lib
 sci-libs/gotoblas2:incblas - Build the CBLAS interface
 sci-libs/gotoblas2:int64 - Build the 64 bits integer library
 sci-libs/gsl:cblas-external - Link gsl with external cblas provided by (virtual/cblas) instead of shipped internal version
-sci-libs/gsl:int64 - Build the 64 bits integer library
 sci-libs/itk:itkv3compat - Enable compatibility with ITK version 3
 sci-libs/itk:review - Enable compilation of methods under review
 sci-libs/itk:vtkglue - PLEASE FIX MY DESCRIPTION

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

[Justin Lecher]

commit:     36f499686a6d8348ef95adfbfeb35ce5c944a76a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 26 08:15:29 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 26 08:15:29 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=36f49968

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index f4769675b..944bce6f4 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -269,6 +269,7 @@ sci-mathematics/gambit:X - Enable gui support using wxWidgets.
 sci-mathematics/gap:xtom - Automatically generated description for xtom
 sci-mathematics/gismo:doc - Build doxygen-documentation
 sci-mathematics/gismo:examples - Build examples
+sci-mathematics/gismo:vtk - Build plug-in for sci-mathematics/axel-vtkview
 sci-mathematics/htk:hdecode - Install HDecode, a large vocabulary word recogniser
 sci-mathematics/htk:hlmtools - Install the tools for manipulation of language models
 sci-mathematics/htk:hslab - Install HSLab a label editor for speech label manipulation

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

[Justin Lecher]

commit:     5a63b5476dc67e4c77f4da804d46d95991926210
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 26 08:37:21 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 26 08:37:21 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5a63b547

Drop empty comments

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/package.mask | 39 +--------------------------------------
 1 file changed, 1 insertion(+), 38 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3594f7ed7..53aeb5548 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,49 +34,12 @@
 # rev dep absent
 sci-mathematics/scilab
 
-# Justin Lecher <jlec@gentoo.org> (24 April 2016)
-# rev dep missing keywords
-
-# Justin Lecher <jlec@gentoo.org> (9 Feb 2016)
-# rev dep masked
-
-# Andreas K. Huettel <dilfridge@gentoo.org> (1 Nov 2014)
-# Lab::Instrument and Lab::Tools provided as separate packages
-# are way outdated. These are now supplied as parts of the package
-# Lab::Measurement (dev-perl/Lab-Measurement in the main portage
-# tree). Masked for removal.
-
-# Jauhien Piatlicki <jauhien@gentoo.org> (13 Sep 2014)
-# dev-python/pythonocc-0.5 works only with sci-libs/opencascade-6.3
-# which is not available in the tree, see bug #522678
-# mask until bug is not fixed
-
-# Honza Macháček <Hloupy.Honza@centrum.cz> (17 June 2013)
-# bigdft moved from sci-libs to sci-physics
-# sci-physics/abinit now uses sci-libs/bigdft-abi instead
-# sci-libs/bigdft should be deleted in 30 days
-
-# Justin Lecher <jlec@gentoo.org> (03 March 2013)
-# Missing deps
-
-# Justin Lecher <jlec@gentoo.org> (28 Apr 2012)
-# Doesn't install pkg-config files, which many packages rely on
-=sci-libs/mmdb-1.24.20111208
-
 # Sebasien Fabbro <bicatali@gentoo.org> (10 Mar 2012)
 # incompatible API with previous versions of metis (4)
 # masked until reverse depedencies are fixed
 >=sci-libs/parmetis-4
 
-# Justin Lecher <jlec@gentoo.org> (24 Jun 2011)
-# paraview dep is masked
-
 # Sebastien Fabbro <bicatali@gentoo.org> (23 Aug 2011)
-# mask old blas from main tree to allow smoother transition to 
+# mask old blas from main tree to allow smoother transition to
 # new blas/lapack framework
 =sci-libs/blas-reference-20070226*
-
-
-# Justin Lecher <jlec@gentoo.org> (11 May 2009)
-# work in progress 
-=sci-chemistry/almost-1.0.3-r1

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

[Justin Lecher]

commit:     e98434a5b0f94c8ce4124a9566fe3e053d277e8d
Author:     Alessandro Barbieri <ale.barbio <AT> alice <DOT> it>
AuthorDate: Fri Apr 14 09:21:50 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Apr 14 09:21:50 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e98434a5

added CeCILL-B license to MISC-FREE license group (#775)

 profiles/license_groups | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/license_groups b/profiles/license_groups
index 78ea7d424..d41f4584e 100644
--- a/profiles/license_groups
+++ b/profiles/license_groups
@@ -1 +1,2 @@
 EULA ACML-EULA AMD-APPSDK NVIDIA-gdk NVIDIA-CUDA OpenSIFT
+MISC-FREE CeCILL-B

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

[Justin Lecher]

commit:     3538c3886c835f8a449bfe4bcf3bb8dc8c7c5c6a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Apr 14 19:17:00 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Apr 14 19:17:09 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3538c388

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 944bce6f4..7eb110061 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -262,9 +262,13 @@ sci-mathematics/Macaulay2:optimization - Disable to build with -O0 for debugging
 sci-mathematics/acl2:books - build community books, the canonical collection of open-source libraries
 sci-mathematics/dolfin:cgal - Adds support for geometric algorithms with sci-mathematics/cgal
 sci-mathematics/dolfin:cholmod - Adds support for sparse Cholesky factorization with sci-libs/cholmod
+sci-mathematics/dolfin:hdf5 - Adds support for sci-libs/hdf5
 sci-mathematics/dolfin:parmetis - Adds support for parallel graph partitioning with sci-libs/parmetis
+sci-mathematics/dolfin:petsc - Adds support for numerical linear algebra toolkit sci-mathematics/petsc
 sci-mathematics/dolfin:scotch - Adds support for graph partitioning with sci-libs/scotch
+sci-mathematics/dolfin:trilinos - Adds support for numerical linear algebra toolkit sci-libs/trilinos
 sci-mathematics/dolfin:umfpack - Adds support for sparse solving with sci-libs/umfpack
+sci-mathematics/dolfin:vtk - Adds support for the visualization toolkit sci-libs/vtk
 sci-mathematics/gambit:X - Enable gui support using wxWidgets.
 sci-mathematics/gap:xtom - Automatically generated description for xtom
 sci-mathematics/gismo:doc - Build doxygen-documentation

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

[Justin Lecher]

commit:     313ba7e9860a3e0c9534ea93e5813317fb066e56
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 30 07:46:53 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 30 07:46:58 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=313ba7e9

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 7eb110061..27951069f 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -312,6 +312,7 @@ sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-mi
 sci-misc/hfst:sfst - Add optional support for sfst backend library (sci-misc/sfst)
 sci-misc/hfst:xml - Include parsers for grammars and formats that require XML support
 sci-misc/kaldi:cuda - Build with CUDA support.
+sci-misc/kaldi:double-precision - Build in double precision mode.
 sci-physics/abinit:atompaw - Enable support for atompaw, a Projector Augmented Waves atomic data generator
 sci-physics/abinit:bigdft - Enable support for BigDFT, DFT package using wavelet basis set
 sci-physics/abinit:cuda - Enable support for nVidia CUDA

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

[Justin Lecher]

commit:     811c2c67535c8905ae1bf784a8e1ea65fc6812e4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jul  9 13:58:50 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jul  9 13:58:54 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=811c2c67

Update local USE description

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/use.local.desc | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 6983341c9..6d7dd0143 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -221,8 +221,9 @@ sci-libs/nibabel:dicom - Adds limited read support for the DICOM imaging format.
 sci-libs/oasa:cairo - Add support for Cairo graphics library using dev-python/pycairo
 sci-libs/openblas:dynamic - Build dynamic architecture detection at run time (for multi targets)
 sci-libs/openblas:int64 - Build the 64 bits integer library
-sci-libs/pagmo:kepler - Automatically generated description for kepler
-sci-libs/pagmo:nlopt - Automatically generated description for nlopt
+sci-libs/pagmo:eigen - Use eigen, a c++ linear algebra library, for algorithms like CAMES
+sci-libs/pagmo:ipopt - Use ipopt, a interior-point optimizer
+sci-libs/pagmo:nlopt - Use nlopt, a non-linear optimization library
 sci-libs/parmetis:double-precision - Floating-point operation done as double precision
 sci-libs/parmetis:int64 - Build the 64 bits integer library (needed for > 2^31 vertices)
 sci-libs/scikits_image:freeimage - Enable support for image i/o via media-libs/freeimage

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

[David Seifert]

commit:     afb1b3ebb8686303d310fb93970aed37f6f6b012
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Sep  7 20:58:30 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Sep  7 20:58:30 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=afb1b3eb

profiles: update use.local.desc for sci-libs/dealii flags

 profiles/use.local.desc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 565f542eb..f5dcc29e0 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -149,6 +149,7 @@ sci-libs/clblas:performance - Copy performance scripts that can measure and grap
 sci-libs/clfft:callback_client - Build a command line clFFT client program that tests callback functionality.
 sci-libs/clfft:client - Build a command line clFFT client program.
 sci-libs/clrng:client - Build a command line clRNG client program.
+sci-libs/dealii:adolc - Adds support for ADOL-C (sci-libs/adolc)
 sci-libs/dealii:arpack - Adds support for ARPACK (sci-libs/arpack)
 sci-libs/dealii:c++11 - Compile the library with -std=c++11
 sci-libs/dealii:debug - Build an additional debug library with extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see <http://www.gentoo.org/proj/en/qa/backtraces.xml>
@@ -156,6 +157,7 @@ sci-libs/dealii:mesh_converter - Build and install the mesh_converter executable
 sci-libs/dealii:metis - Add support for metis (sci-libs/metis)
 sci-libs/dealii:mumps - Add support for mumps (sci-libs/mumps)
 sci-libs/dealii:muparser - Add support for muparser (dev-cpp/muParser)
+sci-libs/dealii:nanoflann - Adds support for nanoflann (sci-libs/nanoflann)
 sci-libs/dealii:opencascade - Add support for opencascade (sci-libs/opencascade)
 sci-libs/dealii:p4est - Add support for p4est (sci-mathematics/p4est)
 sci-libs/dealii:parameter_gui - Build and install the parameter_gui executable

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

[David Seifert]

commit:     9185fe6eceba00773c1bff591c322dec33a8e9de
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 14 19:40:51 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Oct 14 19:40:51 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9185fe6e

profiles: update use.local.desc for sci-libs/dealii flags

 profiles/use.local.desc | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index f5dcc29e0..306ae2d81 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -151,7 +151,9 @@ sci-libs/clfft:client - Build a command line clFFT client program.
 sci-libs/clrng:client - Build a command line clRNG client program.
 sci-libs/dealii:adolc - Adds support for ADOL-C (sci-libs/adolc)
 sci-libs/dealii:arpack - Adds support for ARPACK (sci-libs/arpack)
+sci-libs/dealii:assimp - Add support for assimp (media-libs/assimp)
 sci-libs/dealii:c++11 - Compile the library with -std=c++11
+sci-libs/dealii:cuda - Add support for cuda assimp (dev-util/nvidia-cuda-sdk)
 sci-libs/dealii:debug - Build an additional debug library with extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see <http://www.gentoo.org/proj/en/qa/backtraces.xml>
 sci-libs/dealii:mesh_converter - Build and install the mesh_converter executable
 sci-libs/dealii:metis - Add support for metis (sci-libs/metis)
@@ -164,6 +166,7 @@ sci-libs/dealii:parameter_gui - Build and install the parameter_gui executable
 sci-libs/dealii:petsc - Add support for petsc (sci-mathematics/petsc)
 sci-libs/dealii:slepc - Add support for slepc (sci-mathematics/slepc)
 sci-libs/dealii:sparse - Add support for suitesparse (sci-libs/suitesparse)
+sci-libs/dealii:sundials - Add support for sundials assimp (sci-libs/sundials)
 sci-libs/dealii:tbb - Add threading support with the help of the tbb library (dev-cpp/tbb)
 sci-libs/dealii:trilinos - Add support for trilinos (sci-libs/trilinos)
 sci-libs/etsf_io:pic - Compile Position Independent Code

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

[Justin Lecher]

commit:     97eff1b24282f212586542effa1efb3eb177e877
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 27 20:26:08 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 27 20:39:37 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=97eff1b2

Unmask scilab

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/package.mask | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 53aeb5548..73022d876 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,10 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Justin Lecher <jlec@gentoo.org> (24 April 2016)
-# rev dep absent
-sci-mathematics/scilab
-
 # Sebasien Fabbro <bicatali@gentoo.org> (10 Mar 2012)
 # incompatible API with previous versions of metis (4)
 # masked until reverse depedencies are fixed

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

[Justin Lecher]

commit:     eabd051f313ca258d9df3ca00c884709ee634c14
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  2 11:18:45 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr  2 11:20:24 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=eabd051f

Drop deprecated arches

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 profiles/arch.list | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/arch.list b/profiles/arch.list
index 64e864380..a917db833 100644
--- a/profiles/arch.list
+++ b/profiles/arch.list
@@ -7,10 +7,8 @@ hppa
 ia64
 m68k
 mips
-nios2
 ppc
 ppc64
-riscv
 s390
 sh
 sparc

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

[Horea Christian]

commit:     62fbfe001d920e7a4cd50b5548e721273f96ac8d
Author:     Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Tue Jun 26 14:04:39 2018 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jun 26 14:05:30 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=62fbfe00

Corrected hard masking dates

 profiles/package.mask | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3b55d3b32..37d4fda81 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,11 +30,11 @@
 
 #--- END OF EXAMPLES ---
 
-# Horea Christian <horea.christ@gmail.com> (10 Mar 2012)
+# Horea Christian <horea.christ@gmail.com> (26 Jun 2018)
 # All versions depend on hard-masked sci-biology/afni.
 sci-biology/samri
 
-# Horea Christian <horea.christ@gmail.com> (10 Mar 2012)
+# Horea Christian <horea.christ@gmail.com> (26 Jun 2018)
 # Serious bundling issues, upstream does not support Gentoo
 # or more generally unbundling. Masked until unbundling
 # efforts ( https://github.com/afni/afni/pull/60 ) come to

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

[Horea Christian]

commit:     2fbc1436200a13edf955d5c4b3e26446d8694b88
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Nov 25 18:32:11 2019 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Nov 25 18:32:40 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2fbc1436

profiles: no longer propagating AFNI mask to SAMRI

	Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index ce89ca929..f27070492 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,10 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Horea Christian <horea.christ@gmail.com> (26 Jun 2018)
-# All versions depend on hard-masked sci-biology/afni.
-sci-biology/samri
-
 # Horea Christian <horea.christ@gmail.com> (26 Jun 2018)
 # Serious bundling issues, upstream does not support Gentoo
 # or more generally unbundling. Masked until unbundling

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

[Horea Christian]

commit:     672523049ae3ee4ca1a32647141ae0c1b0a949b3
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Mar 30 03:15:22 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Mar 30 03:15:22 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=67252304

profiles: remove SuperH, analogous to Gentoo Main

https://gitweb.gentoo.org/repo/gentoo.git/commit/profiles/arch.list?id=bd3492f8e8d934a93170df401d53ceea3d313471

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/arch.list | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/arch.list b/profiles/arch.list
index c4fa6d070..d3ed9c37e 100644
--- a/profiles/arch.list
+++ b/profiles/arch.list
@@ -9,7 +9,6 @@ mips
 ppc
 ppc64
 s390
-sh
 sparc
 x86
 

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

[Horea Christian]

commit:     5d3150e4329e87b730eab18dfaab0e02693857b2
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Mar 30 04:46:57 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Mar 30 04:46:57 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5d3150e4

profiles: removed deprecated masking

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index f27070492..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,12 +29,3 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
-
-# Horea Christian <horea.christ@gmail.com> (26 Jun 2018)
-# Serious bundling issues, upstream does not support Gentoo
-# or more generally unbundling. Masked until unbundling
-# efforts ( https://github.com/afni/afni/pull/60 ) come to
-# fruition.
-=sci-biology/afni-19.0.21
-=sci-biology/afni-18.1.04
-

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

[Aisha Tammy]

commit:     32bf481890f13f922f38dbcd5d6866eb8b934bbd
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Wed Oct 14 22:30:53 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Wed Oct 14 22:31:51 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=32bf4818

profiles/package.mask: mask broken reverse deps of rtree

rtree got dropped from ::gentoo

Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 profiles/package.mask | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..b9fc47a55 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,14 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Aisha Tammy <gentoo@aisha.cc> (14 Oct 2020)
+# Mask packages depending on sci-libs/rtree
+# as rtree got dropped from ::gentoo
+dev-python/fslpy
+dev-python/trimesh
+sci-biology/fsl
+sci-biology/samri
+sci-visualization/fsleyes-props
+sci-visualization/fsleyes-widgets
+sci-visualization/fsleyes

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

[Horea Christian]

commit:     e96d09763572adc173da9618119f3f4cd1e1e903
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Oct 19 22:05:57 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Oct 19 22:05:57 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e96d0976

profiles/package.mask: rtree was not removed from ::gentoo

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index b9fc47a55..56b672d8d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,13 +30,3 @@
 
 #--- END OF EXAMPLES ---
 
-# Aisha Tammy <gentoo@aisha.cc> (14 Oct 2020)
-# Mask packages depending on sci-libs/rtree
-# as rtree got dropped from ::gentoo
-dev-python/fslpy
-dev-python/trimesh
-sci-biology/fsl
-sci-biology/samri
-sci-visualization/fsleyes-props
-sci-visualization/fsleyes-widgets
-sci-visualization/fsleyes

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

[Horea Christian]

commit:     1e541f5984504720364352bbe6388fe1842d8bde
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue Oct 20 17:12:25 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Oct 20 17:12:25 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1e541f59

profiles/package.use.mask: packages no longer distributed in ::science

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.use.mask | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 4814b71b9..d8b365654 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -15,11 +15,6 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
-# Matthias Maier <tamiko@gentoo.org) (25 May 2017)
-# sci-libs/parmetis-4* is masked
-sci-mathematics/petsc metis
-sci-libs/dealii metis
-
 # Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
 # doesn't link with plotutils-2.6
 sci-physics/qcl plotutils

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

[Aisha Tammy]

commit:     93e5fa46472c9eb577ccb2430babe235e839d6e6
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Sun Nov 22 00:48:27 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Sun Nov 22 00:48:27 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=93e5fa46

profiles/package.mask: mask unfetchable

Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 profiles/package.mask | 144 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 144 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..0b30ebda0 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,147 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Aisha Tammy <gentoo@aisha.cc> (2020-11-19)
+# mask unfetchable packages until someone fixes.
+app-doc/scalapack-docs
+dev-java/jgraphx
+dev-java/jgraphx
+dev-java/jgraphx
+dev-lang/conceptual
+dev-lang/pgi
+dev-ml/lacaml
+dev-perl/Bio-EnsEMBL
+dev-python/PyVISA-py
+dev-python/PyVISA-py
+dev-python/snakemake
+dev-python/xgboost
+dev-util/f90cache
+sci-biology/BBmap
+sci-biology/BBmap
+sci-biology/BBmap
+sci-biology/BBmap
+sci-biology/BBmap
+sci-biology/EBARDenovo
+sci-biology/ESTate
+sci-biology/FLASH
+sci-biology/GAL
+sci-biology/ICC
+sci-biology/IMAGE
+sci-biology/KING
+sci-biology/MagicViewer
+sci-biology/MeV
+sci-biology/MolBioLib
+sci-biology/MuSeqBox
+sci-biology/NGSEPcore-bin
+sci-biology/NGSEPplugin-bin
+sci-biology/OBO-Edit
+sci-biology/OBO-Edit
+sci-biology/ORFcor
+sci-biology/RSeQC
+sci-biology/SPAdes
+sci-biology/SPAdes
+sci-biology/SnpEff
+sci-biology/VelvetOptimiser
+sci-biology/aghermann
+sci-biology/argo-bin
+sci-biology/argo-bin
+sci-biology/bambino
+sci-biology/bambino
+sci-biology/beagle
+sci-biology/blue
+sci-biology/blue
+sci-biology/cd-hit-auxtools
+sci-biology/cgview-bin
+sci-biology/clover
+sci-biology/cnrun
+sci-biology/conrad
+sci-biology/cortex_var
+sci-biology/cross_genome
+sci-biology/dawg
+sci-biology/ePCR
+sci-biology/ensembl-tools
+sci-biology/estscan
+sci-biology/eval
+sci-biology/ffindex
+sci-biology/fsa
+sci-biology/gap2caf
+sci-biology/geneid
+sci-biology/generecon
+sci-biology/genomeview-bin
+sci-biology/gfftools
+sci-biology/glean
+sci-biology/graf-bin
+sci-biology/hydra-sv
+sci-biology/jannovar
+sci-biology/jtreeview-bin
+sci-biology/jtreeview
+sci-biology/kat
+sci-biology/kat
+sci-biology/kraken
+sci-biology/lucy
+sci-biology/manatee-igs
+sci-biology/manatee-jcvi
+sci-biology/mavid
+sci-biology/mreps
+sci-biology/mrsfast
+sci-biology/pairagon
+sci-biology/polyphen
+sci-biology/primerD
+sci-biology/prokka
+sci-biology/pysamstats
+sci-biology/quast
+sci-biology/reptile
+sci-biology/scaffold_builder
+sci-biology/sgp2
+sci-biology/skewer-bin
+sci-biology/smalt
+sci-biology/snphylo
+sci-biology/sra_sdk
+sci-biology/staden_doc
+sci-biology/staden_doc
+sci-biology/subread
+sci-biology/swissknife
+sci-biology/tablet-bin
+sci-biology/trim_galore
+sci-biology/twinscan
+sci-biology/vague-bin
+sci-biology/wcd
+sci-biology/wgs_tools
+sci-chemistry/camshift
+sci-chemistry/cpmgfit
+sci-chemistry/ctffind
+sci-chemistry/curvefit
+sci-chemistry/dssp2pdb
+sci-chemistry/mddnmr
+sci-chemistry/modelfree
+sci-chemistry/nmrpipe
+sci-chemistry/polygon
+sci-chemistry/smmp
+sci-chemistry/talosn
+sci-chemistry/talosn
+sci-chemistry/trajng
+sci-libs/amber99sb_phipsi
+sci-libs/amber99sbnmr-ildn
+sci-libs/ccif
+sci-libs/etsf_io
+sci-libs/etsf_io
+sci-libs/factory
+sci-libs/fdlibm
+sci-libs/fgsl
+sci-libs/libfac
+sci-libs/lwpr
+sci-libs/modglue
+sci-libs/superlu_dist
+sci-mathematics/Macaulay2
+sci-mathematics/freefem++
+sci-mathematics/lattE-macchiato
+sci-mathematics/pff
+sci-misc/kaldi
+sci-misc/kaldi
+sci-misc/kotus-sanalista
+sci-physics/fullprof-bin
+sci-physics/openmx
+sci-physics/openmx
+sci-physics/uproot
+x11-libs/tr

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

[Aisha Tammy]

commit:     9b1dbbcb8f3c41e154c1b87508c3cfec9e726d29
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Sun Nov 22 00:52:22 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Sun Nov 22 00:52:22 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9b1dbbcb

profiles/package.mask: remove duplicate masks

Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 profiles/package.mask | 66 +++++++++++++++++++--------------------------------
 1 file changed, 24 insertions(+), 42 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 0b30ebda0..99e38f028 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,51 +34,20 @@
 # mask unfetchable packages until someone fixes.
 app-doc/scalapack-docs
 dev-java/jgraphx
-dev-java/jgraphx
-dev-java/jgraphx
 dev-lang/conceptual
 dev-lang/pgi
 dev-ml/lacaml
 dev-perl/Bio-EnsEMBL
 dev-python/PyVISA-py
-dev-python/PyVISA-py
 dev-python/snakemake
 dev-python/xgboost
 dev-util/f90cache
-sci-biology/BBmap
-sci-biology/BBmap
-sci-biology/BBmap
-sci-biology/BBmap
-sci-biology/BBmap
-sci-biology/EBARDenovo
-sci-biology/ESTate
-sci-biology/FLASH
-sci-biology/GAL
-sci-biology/ICC
-sci-biology/IMAGE
-sci-biology/KING
-sci-biology/MagicViewer
-sci-biology/MeV
-sci-biology/MolBioLib
-sci-biology/MuSeqBox
-sci-biology/NGSEPcore-bin
-sci-biology/NGSEPplugin-bin
-sci-biology/OBO-Edit
-sci-biology/OBO-Edit
-sci-biology/ORFcor
-sci-biology/RSeQC
-sci-biology/SPAdes
-sci-biology/SPAdes
-sci-biology/SnpEff
-sci-biology/VelvetOptimiser
 sci-biology/aghermann
 sci-biology/argo-bin
-sci-biology/argo-bin
-sci-biology/bambino
 sci-biology/bambino
+sci-biology/BBmap
 sci-biology/beagle
 sci-biology/blue
-sci-biology/blue
 sci-biology/cd-hit-auxtools
 sci-biology/cgview-bin
 sci-biology/clover
@@ -87,12 +56,16 @@ sci-biology/conrad
 sci-biology/cortex_var
 sci-biology/cross_genome
 sci-biology/dawg
-sci-biology/ePCR
+sci-biology/EBARDenovo
 sci-biology/ensembl-tools
+sci-biology/ePCR
+sci-biology/ESTate
 sci-biology/estscan
 sci-biology/eval
 sci-biology/ffindex
+sci-biology/FLASH
 sci-biology/fsa
+sci-biology/GAL
 sci-biology/gap2caf
 sci-biology/geneid
 sci-biology/generecon
@@ -101,18 +74,28 @@ sci-biology/gfftools
 sci-biology/glean
 sci-biology/graf-bin
 sci-biology/hydra-sv
+sci-biology/ICC
+sci-biology/IMAGE
 sci-biology/jannovar
-sci-biology/jtreeview-bin
 sci-biology/jtreeview
+sci-biology/jtreeview-bin
 sci-biology/kat
-sci-biology/kat
+sci-biology/KING
 sci-biology/kraken
 sci-biology/lucy
+sci-biology/MagicViewer
 sci-biology/manatee-igs
 sci-biology/manatee-jcvi
 sci-biology/mavid
+sci-biology/MeV
+sci-biology/MolBioLib
 sci-biology/mreps
 sci-biology/mrsfast
+sci-biology/MuSeqBox
+sci-biology/NGSEPcore-bin
+sci-biology/NGSEPplugin-bin
+sci-biology/OBO-Edit
+sci-biology/ORFcor
 sci-biology/pairagon
 sci-biology/polyphen
 sci-biology/primerD
@@ -120,20 +103,23 @@ sci-biology/prokka
 sci-biology/pysamstats
 sci-biology/quast
 sci-biology/reptile
+sci-biology/RSeQC
 sci-biology/scaffold_builder
 sci-biology/sgp2
 sci-biology/skewer-bin
 sci-biology/smalt
+sci-biology/SnpEff
 sci-biology/snphylo
+sci-biology/SPAdes
 sci-biology/sra_sdk
 sci-biology/staden_doc
-sci-biology/staden_doc
 sci-biology/subread
 sci-biology/swissknife
 sci-biology/tablet-bin
 sci-biology/trim_galore
 sci-biology/twinscan
 sci-biology/vague-bin
+sci-biology/VelvetOptimiser
 sci-biology/wcd
 sci-biology/wgs_tools
 sci-chemistry/camshift
@@ -147,13 +133,11 @@ sci-chemistry/nmrpipe
 sci-chemistry/polygon
 sci-chemistry/smmp
 sci-chemistry/talosn
-sci-chemistry/talosn
 sci-chemistry/trajng
-sci-libs/amber99sb_phipsi
 sci-libs/amber99sbnmr-ildn
+sci-libs/amber99sb_phipsi
 sci-libs/ccif
 sci-libs/etsf_io
-sci-libs/etsf_io
 sci-libs/factory
 sci-libs/fdlibm
 sci-libs/fgsl
@@ -161,15 +145,13 @@ sci-libs/libfac
 sci-libs/lwpr
 sci-libs/modglue
 sci-libs/superlu_dist
-sci-mathematics/Macaulay2
 sci-mathematics/freefem++
 sci-mathematics/lattE-macchiato
+sci-mathematics/Macaulay2
 sci-mathematics/pff
 sci-misc/kaldi
-sci-misc/kaldi
 sci-misc/kotus-sanalista
 sci-physics/fullprof-bin
 sci-physics/openmx
-sci-physics/openmx
 sci-physics/uproot
 x11-libs/tr

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

[Aisha Tammy]

commit:     2888a7a8f1c19e732f87768e273b10e28e05a488
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Sun Nov 22 01:17:14 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Sun Nov 22 01:17:14 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2888a7a8

profiles/package.mask: mask more reverse deps

Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 99e38f028..1f9458c22 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -49,6 +49,7 @@ sci-biology/BBmap
 sci-biology/beagle
 sci-biology/blue
 sci-biology/cd-hit-auxtools
+sci-biology/cegma
 sci-biology/cgview-bin
 sci-biology/clover
 sci-biology/cnrun
@@ -90,11 +91,13 @@ sci-biology/mavid
 sci-biology/MeV
 sci-biology/MolBioLib
 sci-biology/mreps
+sci-biology/mRNAmarkup
 sci-biology/mrsfast
 sci-biology/MuSeqBox
 sci-biology/NGSEPcore-bin
 sci-biology/NGSEPplugin-bin
 sci-biology/OBO-Edit
+sci-biology/ONTO-PERL
 sci-biology/ORFcor
 sci-biology/pairagon
 sci-biology/polyphen
@@ -116,6 +119,7 @@ sci-biology/staden_doc
 sci-biology/subread
 sci-biology/swissknife
 sci-biology/tablet-bin
+sci-biology/TransDecoder
 sci-biology/trim_galore
 sci-biology/twinscan
 sci-biology/vague-bin
@@ -131,6 +135,7 @@ sci-chemistry/mddnmr
 sci-chemistry/modelfree
 sci-chemistry/nmrpipe
 sci-chemistry/polygon
+sci-chemistry/relion
 sci-chemistry/smmp
 sci-chemistry/talosn
 sci-chemistry/trajng

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

[Horea Christian]

commit:     5aa51d487d13d5cd22f5111f355c1814fa24e23b
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Nov 28 09:13:32 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Nov 28 09:13:32 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5aa51d48

profiles/package.mask: removed packages

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1f9458c22..793206041 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -143,10 +143,8 @@ sci-libs/amber99sbnmr-ildn
 sci-libs/amber99sb_phipsi
 sci-libs/ccif
 sci-libs/etsf_io
-sci-libs/factory
 sci-libs/fdlibm
 sci-libs/fgsl
-sci-libs/libfac
 sci-libs/lwpr
 sci-libs/modglue
 sci-libs/superlu_dist

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

[Aisha Tammy]

commit:     fbd14207e9778ca72d3eb17e0d223992db78c708
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Dec 20 10:07:48 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Sun Dec 20 23:29:37 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fbd14207

profiles/pakcage.mask: cleanup

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

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 6a455be74..af612da87 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,7 +38,6 @@ dev-lang/conceptual
 dev-lang/pgi
 dev-ml/lacaml
 dev-perl/Bio-EnsEMBL
-dev-python/PyVISA-py
 dev-python/snakemake
 dev-python/xgboost
 dev-util/f90cache

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

[Horea Christian]

commit:     2eb50600aa460c5b00e0a3baa4868675c22291ac
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Dec 25 20:24:39 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Dec 25 20:24:39 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2eb50600

profiles/package.use.mask: removed mask for dropped package

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.use.mask | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index d8b365654..a3d897332 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -23,10 +23,6 @@ sci-physics/qcl plotutils
 # icc and ifc don't work on no-multilib
 sci-biology/estscan icc ifc
 
-# Justin Lecher <jlec@gntoo.org> (06 Jan 2014)
-# Missing dep dev-python/scikits-cuda
-sci-biology/mne-python cuda
-
 # Andreas Schäfer <gentryx@gmx.de> (21 Nov 2013)
 # cuda only works on x86 and amd64
 sys-cluster/openmpi -cuda

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

[Benda XU]

commit:     e7479bc3d8b9d1bedeca89b98cc4013486f2bf93
Author:     Benda Xu <heroxbd <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 27 02:14:00 2020 +0000
Commit:     Benda XU <heroxbd <AT> gentoo <DOT> org>
CommitDate: Sun Dec 27 02:14:00 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e7479bc3

package.mask: mask hdf-java for removal.

The ebuild calls for deep refactorization to accommodate upstream.

Bug: https://bugs.gentoo.org/761055
Bug: https://bugs.gentoo.org/640956
Signed-off-by: Benda Xu <heroxbd <AT> gentoo.org>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 988e25f2d..bd1464055 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,12 @@
 
 #--- END OF EXAMPLES ---
 
+# Benda Xu <heroxbd@gentoo.org> (2020-12-27)
+# hdf-java is failing.  Upstream has splitted the software into
+# HDFView and HDF Java.  Mask for removal.
+# https://bugs.gentoo.org/761055
+dev-java/hdf-java
+
 # Aisha Tammy <gentoo@aisha.cc> (2020-11-19)
 # mask unfetchable packages until someone fixes.
 app-doc/scalapack-docs

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

[Aisha Tammy]

commit:     431cd134e2cb0a2f7b4adb9e4c6c14db7e13f892
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Dec 29 18:20:34 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Dec 29 18:35:42 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=431cd134

profiles/* cleanup

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Closes: https://github.com/gentoo/sci/pull/1001
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 profiles/arch.list        |  32 ---------
 profiles/categories       | 163 ----------------------------------------------
 profiles/package.use.mask |   6 +-
 profiles/profiles.desc    |   1 -
 4 files changed, 1 insertion(+), 201 deletions(-)

diff --git a/profiles/arch.list b/profiles/arch.list
deleted file mode 100644
index d3ed9c37e..000000000
--- a/profiles/arch.list
+++ /dev/null
@@ -1,32 +0,0 @@
-alpha
-amd64
-arm
-arm64
-hppa
-ia64
-m68k
-mips
-ppc
-ppc64
-s390
-sparc
-x86
-
-# Prefix keywords
-ppc-aix
-amd64-linux
-arm-linux
-arm64-linux
-ppc64-linux
-x86-linux
-ppc-macos
-x86-macos
-x64-macos
-m68k-mint
-sparc-solaris
-sparc64-solaris
-x64-solaris
-x86-solaris
-x86-winnt
-x64-cygwin
-x86-cygwin

diff --git a/profiles/categories b/profiles/categories
deleted file mode 100644
index 3d47d6ca4..000000000
--- a/profiles/categories
+++ /dev/null
@@ -1,163 +0,0 @@
-app-accessibility
-app-admin
-app-antivirus
-app-arch
-app-backup
-app-benchmarks
-app-cdr
-app-crypt
-app-dicts
-app-doc
-app-editors
-app-emacs
-app-emulation
-app-eselect
-app-forensics
-app-i18n
-app-laptop
-app-leechcraft
-app-misc
-app-mobilephone
-app-office
-app-officeext
-app-pda
-app-portage
-app-shells
-app-text
-app-vim
-app-xemacs
-dev-ada
-dev-cpp
-dev-db
-dev-dotnet
-dev-embedded
-dev-erlang
-dev-games
-dev-go
-dev-haskell
-dev-java
-dev-lang
-dev-libs
-dev-lisp
-dev-lua
-dev-ml
-dev-perl
-dev-php
-dev-python
-dev-qt
-dev-ros
-dev-ruby
-dev-scheme
-dev-tcltk
-dev-tex
-dev-texlive
-dev-util
-dev-vcs
-games-action
-games-arcade
-games-board
-games-emulation
-games-engines
-games-fps
-games-kids
-games-misc
-games-mud
-games-puzzle
-games-roguelike
-games-rpg
-games-server
-games-simulation
-games-sports
-games-strategy
-games-util
-gnome-base
-gnome-extra
-gnustep-apps
-gnustep-base
-gnustep-libs
-java-virtuals
-kde-apps
-kde-frameworks
-kde-misc
-kde-plasma
-lxde-base
-lxqt-base
-mail-client
-mail-filter
-mail-mta
-mate-base
-mate-extra
-media-fonts
-media-gfx
-media-libs
-media-plugins
-media-radio
-media-sound
-media-tv
-media-video
-net-analyzer
-net-dialup
-net-dns
-net-firewall
-net-fs
-net-ftp
-net-im
-net-irc
-net-libs
-net-mail
-net-misc
-net-nds
-net-news
-net-nntp
-net-p2p
-net-print
-net-proxy
-net-voip
-net-wireless
-perl-core
-ros-meta
-sci-astronomy
-sci-biology
-sci-calculators
-sci-chemistry
-sci-electronics
-sci-geosciences
-sci-libs
-sci-mathematics
-sci-misc
-sci-physics
-sci-visualization
-sec-policy
-sys-apps
-sys-auth
-sys-block
-sys-boot
-sys-cluster
-sys-devel
-sys-fabric
-sys-firmware
-sys-freebsd
-sys-fs
-sys-kernel
-sys-libs
-sys-power
-sys-process
-virtual
-www-apache
-www-apps
-www-client
-www-misc
-www-plugins
-www-servers
-x11-apps
-x11-base
-x11-drivers
-x11-libs
-x11-misc
-x11-plugins
-x11-proto
-x11-terms
-x11-themes
-x11-wm
-xfce-base
-xfce-extra

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index a3d897332..09d72f798 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 # When you add an entry to the top of this file, add your name, the date, and
@@ -23,10 +23,6 @@ sci-physics/qcl plotutils
 # icc and ifc don't work on no-multilib
 sci-biology/estscan icc ifc
 
-# Andreas Schäfer <gentryx@gmx.de> (21 Nov 2013)
-# cuda only works on x86 and amd64
-sys-cluster/openmpi -cuda
-
 # Andreas Schäfer <gentryx@gmx.de> (21 Nov 2013)
 # cuda only works on x86 and amd64
 sys-cluster/openmpi -cuda

diff --git a/profiles/profiles.desc b/profiles/profiles.desc
deleted file mode 100644
index 8b1378917..000000000
--- a/profiles/profiles.desc
+++ /dev/null
@@ -1 +0,0 @@
-

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

[Aisha Tammy]

commit:     62c5a5911b79576ee4c9dc58090e494a0ba78cc1
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Dec 29 18:36:35 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Dec 29 18:36:35 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=62c5a591

profiles/package.use.mask: remove old openmpi cuda

we no longer have openmpi in ::science

Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 profiles/package.use.mask | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 09d72f798..e26c02c39 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -23,9 +23,6 @@ sci-physics/qcl plotutils
 # icc and ifc don't work on no-multilib
 sci-biology/estscan icc ifc
 
-# Andreas Schäfer <gentryx@gmx.de> (21 Nov 2013)
-# cuda only works on x86 and amd64
-sys-cluster/openmpi -cuda
 # Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
 # gui sandbox error
 dev-lang/conceptual gui

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

[Aisha Tammy]

commit:     343d0e4612a03860391902e672f1370de40433dc
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Wed Dec 30 17:26:10 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Wed Dec 30 17:26:50 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=343d0e46

profiles/package.mask: drop mask on app-doc/scalapack-docs

Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index bd1464055..2bda530c1 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,7 +38,6 @@ dev-java/hdf-java
 
 # Aisha Tammy <gentoo@aisha.cc> (2020-11-19)
 # mask unfetchable packages until someone fixes.
-app-doc/scalapack-docs
 dev-java/jgraphx
 dev-lang/conceptual
 dev-lang/pgi

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

[Aisha Tammy]

commit:     9dd84cc3d2f48f60dae52073161dbf5f12457261
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Dec 31 16:25:33 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Thu Dec 31 16:34:19 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9dd84cc3

profiles/package.mask: unmask ctffind: fixed

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Closes: https://github.com/gentoo/sci/pull/1023
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index f1328ec4c..5011a19c0 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -132,7 +132,6 @@ sci-biology/wcd
 sci-biology/wgs_tools
 sci-chemistry/camshift
 sci-chemistry/cpmgfit
-sci-chemistry/ctffind
 sci-chemistry/curvefit
 sci-chemistry/dssp2pdb
 sci-chemistry/mddnmr

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

[Aisha Tammy]

commit:     a4b080ac2d5c0fb692c47b966eba8257c1df40a9
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Dec 31 16:29:13 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Thu Dec 31 17:22:02 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4b080ac

profiles/package.maks: unmask snakemake: fixed

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Closes: https://github.com/gentoo/sci/pull/1005
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 5011a19c0..9f4968672 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -43,7 +43,6 @@ dev-lang/conceptual
 dev-lang/pgi
 dev-ml/lacaml
 dev-perl/Bio-EnsEMBL
-dev-python/snakemake
 dev-python/xgboost
 dev-util/f90cache
 sci-biology/aghermann

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

[Horea Christian]

commit:     487d6d281b617dc050cb022128435b6794dfba88
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Jan  1 15:29:39 2021 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Jan  3 22:13:54 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=487d6d28

profiles/package.mask: unmask jgraphx, fixed

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
Closes: https://github.com/gentoo/sci/pull/1025

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9f4968672..544cb2b21 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,7 +38,6 @@ dev-java/hdf-java
 
 # Aisha Tammy <gentoo@aisha.cc> (2020-11-19)
 # mask unfetchable packages until someone fixes.
-dev-java/jgraphx
 dev-lang/conceptual
 dev-lang/pgi
 dev-ml/lacaml

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

[Horea Christian]

commit:     17e75e3cb282e3dbb1812b57b241ce7fd947fde7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan  4 15:39:05 2021 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jan  5 06:08:00 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=17e75e3c

profiles/package.mask unmask quast and and pysamstats: fixed

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
Closes: https://github.com/gentoo/sci/pull/1035

 profiles/package.mask | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 544cb2b21..805047cf4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -105,8 +105,6 @@ sci-biology/pairagon
 sci-biology/polyphen
 sci-biology/primerD
 sci-biology/prokka
-sci-biology/pysamstats
-sci-biology/quast
 sci-biology/reptile
 sci-biology/RSeQC
 sci-biology/scaffold_builder

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

[Andrew Ammerlaan]

commit:     929c72e2ece8cc728658b3ef69b08bfe5fc9c2d9
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan  5 13:42:36 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan  5 16:03:39 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=929c72e2

profiles/package.mask: unmask xgboost, fixed

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

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 805047cf4..c8c916a38 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -42,7 +42,6 @@ dev-lang/conceptual
 dev-lang/pgi
 dev-ml/lacaml
 dev-perl/Bio-EnsEMBL
-dev-python/xgboost
 dev-util/f90cache
 sci-biology/aghermann
 sci-biology/argo-bin

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

[Andrew Ammerlaan]

commit:     b2cf53980717f44a589ebeec6978f92ecf9b6077
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 12:26:29 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 12:26:29 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b2cf5398

profiles/package.mask unmask NGSEPcore-bin: fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index c8c916a38..1b48061f1 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -95,7 +95,6 @@ sci-biology/mreps
 sci-biology/mRNAmarkup
 sci-biology/mrsfast
 sci-biology/MuSeqBox
-sci-biology/NGSEPcore-bin
 sci-biology/NGSEPplugin-bin
 sci-biology/OBO-Edit
 sci-biology/ONTO-PERL

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

[Andrew Ammerlaan]

commit:     1d6b9e950fc0c38fc88fa11a0193f74b7003e73c
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 12:39:24 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 12:39:24 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1d6b9e95

profiles/package.mask: remove mask of removed package

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1b48061f1..b49dea9a2 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -95,7 +95,6 @@ sci-biology/mreps
 sci-biology/mRNAmarkup
 sci-biology/mrsfast
 sci-biology/MuSeqBox
-sci-biology/NGSEPplugin-bin
 sci-biology/OBO-Edit
 sci-biology/ONTO-PERL
 sci-biology/ORFcor

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

[Andrew Ammerlaan]

commit:     8e47e38590917df10375a63bc0f448a9114fe8b1
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 18:40:32 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 18:40:32 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8e47e385

profiles/package.mask: drop mask of removed packs

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index b49dea9a2..8618f1cc9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -124,11 +124,8 @@ sci-biology/VelvetOptimiser
 sci-biology/wcd
 sci-biology/wgs_tools
 sci-chemistry/camshift
-sci-chemistry/cpmgfit
-sci-chemistry/curvefit
 sci-chemistry/dssp2pdb
 sci-chemistry/mddnmr
-sci-chemistry/modelfree
 sci-chemistry/nmrpipe
 sci-chemistry/polygon
 sci-chemistry/relion

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

[Andrew Ammerlaan]

commit:     683c2c094694c38c54e8da261c32e9fb159a4ffc
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 19:24:19 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 19:24:19 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=683c2c09

profiles/license_groups: clean up removed license

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/license_groups | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/profiles/license_groups b/profiles/license_groups
index 1d2f8f87a..c505c87d8 100644
--- a/profiles/license_groups
+++ b/profiles/license_groups
@@ -1 +1 @@
-EULA NVIDIA-gdk OpenSIFT
+EULA OpenSIFT

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

[Andrew Ammerlaan]

commit:     95efe2698dcc5078fba8f2966e66645dc3f2a0c7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Jan 15 19:23:42 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Jan 15 19:23:42 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=95efe269

profiles/package.mask: unmask fullprof, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 8e448b584..6051fac9c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -145,5 +145,4 @@ sci-mathematics/lattE-macchiato
 sci-mathematics/Macaulay2
 sci-mathematics/pff
 sci-misc/kotus-sanalista
-sci-physics/fullprof-bin
 sci-physics/openmx

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

[Andrew Ammerlaan]

commit:     3c09d14ced264cf7b48222463ece0d7ab4970816
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Jan 15 20:04:47 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Jan 15 20:04:47 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3c09d14c

profiles/package.mask: unmask openmx, fetching fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 6051fac9c..7c936f3cd 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -145,4 +145,3 @@ sci-mathematics/lattE-macchiato
 sci-mathematics/Macaulay2
 sci-mathematics/pff
 sci-misc/kotus-sanalista
-sci-physics/openmx

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

[Andrew Ammerlaan]

commit:     01aafa72d271b10186473c84a9d4e1b57b6d8196
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 16 10:28:11 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 16 10:28:11 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=01aafa72

profiles/package.mask: unmask conceptual, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index e48586b04..cc73ad6d1 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,7 +38,6 @@ dev-java/hdf-java
 
 # Aisha Tammy <gentoo@aisha.cc> (2020-11-19)
 # mask unfetchable packages until someone fixes.
-dev-lang/conceptual
 dev-lang/pgi
 dev-ml/lacaml
 dev-perl/Bio-EnsEMBL

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

[Andrew Ammerlaan]

commit:     efff12639157f9336e47dbeca2bf7d8eb310b111
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 16 10:42:54 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 16 10:42:54 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=efff1263

profiles/package.mask: unmask lacaml, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 0c1f7b78e..77c85a720 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,7 +38,6 @@ dev-java/hdf-java
 
 # Aisha Tammy <gentoo@aisha.cc> (2020-11-19)
 # mask unfetchable packages until someone fixes.
-dev-ml/lacaml
 dev-perl/Bio-EnsEMBL
 dev-util/f90cache
 sci-biology/aghermann

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

[Andrew Ammerlaan]

commit:     a530380da20881b193482cea43da354f9ca70320
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 16 10:49:14 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 16 10:49:14 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a530380d

profiles/package.mask: unmask Bio-EnsEMBL, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 77c85a720..7652cc6d7 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,7 +38,6 @@ dev-java/hdf-java
 
 # Aisha Tammy <gentoo@aisha.cc> (2020-11-19)
 # mask unfetchable packages until someone fixes.
-dev-perl/Bio-EnsEMBL
 dev-util/f90cache
 sci-biology/aghermann
 sci-biology/argo-bin

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

[Andrew Ammerlaan]

commit:     40dd8efa8d9e6ebdd2e6c00be0e61d0985af4754
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 16 10:53:49 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 16 10:53:49 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=40dd8efa

profiles/package.mask: unmask f90cache, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 7652cc6d7..d7c877efc 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,7 +38,6 @@ dev-java/hdf-java
 
 # Aisha Tammy <gentoo@aisha.cc> (2020-11-19)
 # mask unfetchable packages until someone fixes.
-dev-util/f90cache
 sci-biology/aghermann
 sci-biology/argo-bin
 sci-biology/bambino

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

[Andrew Ammerlaan]

commit:     4b39712af400d866e89c316f14067c1c95d98aa7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 16 20:54:09 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 16 20:54:09 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4b39712a

profiles/package.mask: unmask freefem++, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index d7c877efc..33afc9aa6 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -135,7 +135,6 @@ sci-libs/fgsl
 sci-libs/lwpr
 sci-libs/modglue
 sci-libs/superlu_dist
-sci-mathematics/freefem++
 sci-mathematics/lattE-macchiato
 sci-mathematics/Macaulay2
 sci-mathematics/pff

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

[Andrew Ammerlaan]

commit:     8fde3ceb01aaa208bc07e63ea5504ca03074b88e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 16 21:12:04 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 16 21:12:04 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8fde3ceb

profiles/package.mask: unmask latte-macchiato, fetching fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 33afc9aa6..6501d0332 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -135,6 +135,5 @@ sci-libs/fgsl
 sci-libs/lwpr
 sci-libs/modglue
 sci-libs/superlu_dist
-sci-mathematics/lattE-macchiato
 sci-mathematics/Macaulay2
 sci-mathematics/pff

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

[Andrew Ammerlaan]

commit:     3a05530aa6993bcd80d7b4944ad6fdc208ae3f05
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 16 21:29:25 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 16 21:29:25 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a05530a

profiles/package.mask: unmask Macaulay2, fetching fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 6501d0332..f0127c835 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -135,5 +135,4 @@ sci-libs/fgsl
 sci-libs/lwpr
 sci-libs/modglue
 sci-libs/superlu_dist
-sci-mathematics/Macaulay2
 sci-mathematics/pff

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

[Andrew Ammerlaan]

commit:     94c57738afc6e3cde1be9cc4b013de92cc65bd4a
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 08:18:29 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 08:18:29 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=94c57738

profiles/package.mask: unmask amber99sbnmr, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 34cefe170..e6243349c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -126,8 +126,6 @@ sci-chemistry/polygon
 sci-chemistry/relion
 sci-chemistry/talosn
 sci-chemistry/trajng
-sci-libs/amber99sbnmr-ildn
-sci-libs/amber99sb_phipsi
 sci-libs/ccif
 sci-libs/etsf_io
 sci-libs/fdlibm

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

[Andrew Ammerlaan]

commit:     b031b53fd6b01342cada8f879c53662353606569
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 09:00:45 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 09:00:45 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b031b53f

profiles/package.mask: unmask superflu_dist, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index e6243349c..f71aba9d3 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -132,4 +132,3 @@ sci-libs/fdlibm
 sci-libs/fgsl
 sci-libs/lwpr
 sci-libs/modglue
-sci-libs/superlu_dist

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

[Andrew Ammerlaan]

commit:     fd27d4175f00106edd0513ca15161e7a8ea0de4c
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 09:20:41 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 09:20:41 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fd27d417

profiles/package.mask: unmask lwpr, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 5c0216867..8f326ff0d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -130,4 +130,3 @@ sci-libs/ccif
 sci-libs/etsf_io
 sci-libs/fdlibm
 sci-libs/fgsl
-sci-libs/lwpr

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

[Andrew Ammerlaan]

commit:     2e1ea0a55f7c021a722640134f0edb765b4fe317
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 09:47:09 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 09:47:09 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e1ea0a5

profiles/package.mask: unmask fgsl, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 8f326ff0d..a1c710655 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -129,4 +129,3 @@ sci-chemistry/trajng
 sci-libs/ccif
 sci-libs/etsf_io
 sci-libs/fdlibm
-sci-libs/fgsl

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

[Andrew Ammerlaan]

commit:     87d447752d347d1d23a7f60f964c81e026f76d6e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 10:10:47 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 10:10:47 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=87d44775

profiles/package.mask: unmask sci-libs/fdlibm, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index a1c710655..f9caf85d9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -128,4 +128,3 @@ sci-chemistry/talosn
 sci-chemistry/trajng
 sci-libs/ccif
 sci-libs/etsf_io
-sci-libs/fdlibm

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

[Andrew Ammerlaan]

commit:     47f1374a9444d277a0edac6c0ac5a5f9f57b592a
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 10:41:17 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 10:41:17 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=47f1374a

profiles/package.mask: unmask etsf_io, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index f9caf85d9..1f56558f2 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -127,4 +127,3 @@ sci-chemistry/relion
 sci-chemistry/talosn
 sci-chemistry/trajng
 sci-libs/ccif
-sci-libs/etsf_io

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

[Andrew Ammerlaan]

commit:     bea4e8e07c65947a83e7dc7346963c2e642dff73
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 10:45:31 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 10:45:31 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bea4e8e0

profiles/package.mask: unmask ccif, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1f56558f2..734d3a602 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -126,4 +126,3 @@ sci-chemistry/polygon
 sci-chemistry/relion
 sci-chemistry/talosn
 sci-chemistry/trajng
-sci-libs/ccif

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

[Andrew Ammerlaan]

commit:     4471517843063a3f687783527d0aa1421e813a59
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 11:33:27 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 11:33:27 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=44715178

profiles/package.mask: unmask sci-chemistry/talosn, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 386bdc97c..5d12ccd0f 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -124,4 +124,3 @@ sci-chemistry/mddnmr
 sci-chemistry/nmrpipe
 sci-chemistry/polygon
 sci-chemistry/relion
-sci-chemistry/talosn

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

[Andrew Ammerlaan]

commit:     900d23b0d702db290b339260172107ca4fab69b7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 11:55:19 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 11:55:19 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=900d23b0

profiles/package.mask: unmask relion, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 5d12ccd0f..07e00ce6c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -123,4 +123,3 @@ sci-chemistry/dssp2pdb
 sci-chemistry/mddnmr
 sci-chemistry/nmrpipe
 sci-chemistry/polygon
-sci-chemistry/relion

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

[Andrew Ammerlaan]

commit:     13c1380e5a43caeecdd4bda358148fdb97bd94d1
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:06:36 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:06:36 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=13c1380e

profiles/package.mask: unmask sci-chemistry/nmrpipe, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1b43e59cd..0a12de3f1 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -121,4 +121,3 @@ sci-biology/wgs_tools
 sci-chemistry/camshift
 sci-chemistry/dssp2pdb
 sci-chemistry/mddnmr
-sci-chemistry/nmrpipe

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

[Andrew Ammerlaan]

commit:     e9dba185da97b563ed06e21dedd5c3d25d289b19
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:14:40 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:14:40 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e9dba185

profiles/package.mask: unmask mddnmr

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 0a12de3f1..baae66f83 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -120,4 +120,3 @@ sci-biology/wcd
 sci-biology/wgs_tools
 sci-chemistry/camshift
 sci-chemistry/dssp2pdb
-sci-chemistry/mddnmr

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

[Andrew Ammerlaan]

commit:     c2f0300d2edddae862b6d7bfc815bfc83669bc19
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:25:58 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:25:58 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c2f0300d

profiles/package.mask: unmask sci-biology/wgs_tools, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 829de8c5b..23c3bbb64 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -117,4 +117,3 @@ sci-biology/twinscan
 sci-biology/vague-bin
 sci-biology/VelvetOptimiser
 sci-biology/wcd
-sci-biology/wgs_tools

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

[Andrew Ammerlaan]

commit:     760837298c4a6f676bfbdfec7b9c1edf94dca7ed
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:42:42 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:42:42 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=76083729

profiles/package.mask: unmask sci-biology/wcd, fetch fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 23c3bbb64..9a4d51f34 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -116,4 +116,3 @@ sci-biology/trim_galore
 sci-biology/twinscan
 sci-biology/vague-bin
 sci-biology/VelvetOptimiser
-sci-biology/wcd

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

[Andrew Ammerlaan]

commit:     659c8c5f33507a1e75c78f7877d4527885e02973
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:53:05 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:53:05 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=659c8c5f

profiles/package.mask: unmask sci-biology/VelvetOptimiser, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9a4d51f34..c5e785acf 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -115,4 +115,3 @@ sci-biology/TransDecoder
 sci-biology/trim_galore
 sci-biology/twinscan
 sci-biology/vague-bin
-sci-biology/VelvetOptimiser

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

[Andrew Ammerlaan]

commit:     ee247b86d00a7aae7c1bedf251fa8dbbb92d613b
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:57:29 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:57:29 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ee247b86

profiles/package.mask: unmask sci-biology/vague-bin, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index c5e785acf..4addb8cbf 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -114,4 +114,3 @@ sci-biology/tablet-bin
 sci-biology/TransDecoder
 sci-biology/trim_galore
 sci-biology/twinscan
-sci-biology/vague-bin

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

[Andrew Ammerlaan]

commit:     32b5b2636ca398b395801516ef5ed394059e592f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 13:19:40 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 13:19:40 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=32b5b263

profiles/package.mask: unmask sci-biology/trim_galore, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 04a82cd44..eb4cce984 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -112,4 +112,3 @@ sci-biology/subread
 sci-biology/swissknife
 sci-biology/tablet-bin
 sci-biology/TransDecoder
-sci-biology/trim_galore

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

[Andrew Ammerlaan]

commit:     b97426c0b0bd46a4eb48867e98e16d8175b6fbf0
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 13:31:04 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 13:31:04 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b97426c0

profiles/package.mask: unmask TransDecoder and ffindex, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index eb4cce984..f609137fe 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -59,7 +59,6 @@ sci-biology/ePCR
 sci-biology/ESTate
 sci-biology/estscan
 sci-biology/eval
-sci-biology/ffindex
 sci-biology/FLASH
 sci-biology/fsa
 sci-biology/GAL
@@ -111,4 +110,3 @@ sci-biology/staden_doc
 sci-biology/subread
 sci-biology/swissknife
 sci-biology/tablet-bin
-sci-biology/TransDecoder

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

[Andrew Ammerlaan]

commit:     ae869079e23d2b0bd30a23470c1fd1bbbae4abd8
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 13:48:25 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 13:48:42 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ae869079

profiles/package.mask: unmask sci-biology/tablet-bin, fetching fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index f609137fe..6b2dffda9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -109,4 +109,3 @@ sci-biology/sra_sdk
 sci-biology/staden_doc
 sci-biology/subread
 sci-biology/swissknife
-sci-biology/tablet-bin

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

[Andrew Ammerlaan]

commit:     2145b004fc4744aefb76a2dcacc7524764a2a199
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 09:47:59 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 09:47:59 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2145b004

profiles/package.mask: unmask sci-biology/RSeQC, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 449547311..c5743f05e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -97,4 +97,3 @@ sci-biology/polyphen
 sci-biology/primerD
 sci-biology/prokka
 sci-biology/reptile
-sci-biology/RSeQC

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

[Andrew Ammerlaan]

commit:     76206ae5d8e1863c15d123b47c8310a3dc043914
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 12:17:52 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 12:17:52 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=76206ae5

profiles/package.mask: unmask sci-biology/manatee-igs and sci-biology/manatee-jcvi, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 70da8bb30..302abebb6 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -79,5 +79,3 @@ sci-biology/KING
 sci-biology/kraken
 sci-biology/lucy
 sci-biology/MagicViewer
-sci-biology/manatee-igs
-sci-biology/manatee-jcvi

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

[Andrew Ammerlaan]

commit:     40dfbd8beaf9a552d5ee3eb2583cd8201da8a74d
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 12:32:48 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 12:32:48 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=40dfbd8b

profiles/package.mask: unmask sci-biology/KING, fixed

accedentily included the fix in the previous commit

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 31faa0702..f4540e96e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -74,4 +74,3 @@ sci-biology/IMAGE
 sci-biology/jannovar
 sci-biology/jtreeview
 sci-biology/jtreeview-bin
-sci-biology/KING

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

[Andrew Ammerlaan]

commit:     6ad153c6fc2c20e65bd65650041fe98310e3ef95
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 13:12:55 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 13:12:55 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ad153c6

profiles/package.mask: unmask IMAGE, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/.package.mask.kate-swp | Bin 68 -> 0 bytes
 profiles/package.mask           |   1 -
 2 files changed, 1 deletion(-)

diff --git a/profiles/.package.mask.kate-swp b/profiles/.package.mask.kate-swp
deleted file mode 100644
index e54e3ee5d..000000000
Binary files a/profiles/.package.mask.kate-swp and /dev/null differ

diff --git a/profiles/package.mask b/profiles/package.mask
index 76b2513eb..4eb0cab74 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -70,4 +70,3 @@ sci-biology/glean
 sci-biology/graf-bin
 sci-biology/hydra-sv
 sci-biology/ICC
-sci-biology/IMAGE

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

[Andrew Ammerlaan]

commit:     d8e57519f9315acaf41223b64360f3b4adaaaebc
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 13:55:01 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 13:55:01 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d8e57519

profiles/package.mask: unmask sci-biology/GAL, fetching fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index e6382d12a..d6c8eb6df 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -60,4 +60,3 @@ sci-biology/ESTate
 sci-biology/eval
 sci-biology/FLASH
 sci-biology/fsa
-sci-biology/GAL

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

[Andrew Ammerlaan]

commit:     22fd9753400a18565957fa24daa0b32a54855d66
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 14:11:15 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 14:11:15 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=22fd9753

profiles/package.mask: rmeove mask of removed pack

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index b366f329f..a951d2d34 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -57,4 +57,3 @@ sci-biology/EBARDenovo
 sci-biology/ensembl-tools
 sci-biology/ePCR
 sci-biology/ESTate
-sci-biology/eval

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

[Andrew Ammerlaan]

commit:     5018acd759cf7577a1f67a580e5813b1eafc8dbb
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 14:31:25 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 14:32:45 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5018acd7

sci-biology/cortex_var: fix fetch

still needs patch to build, so no keywords until someone
fixes that

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index c957797cc..0dcabbbca 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -50,3 +50,4 @@ sci-biology/cgview-bin
 sci-biology/clover
 sci-biology/cnrun
 sci-biology/conrad
+

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

[Andrew Ammerlaan]

commit:     e6ef1020a746879a74d24972e2b4420987682722
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 14:33:03 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 14:33:03 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e6ef1020

profiles/package.mask: unmask sci-biology/conrad, fixed

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 0dcabbbca..4b3eb6458 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -49,5 +49,4 @@ sci-biology/cegma
 sci-biology/cgview-bin
 sci-biology/clover
 sci-biology/cnrun
-sci-biology/conrad
 

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

[Benda XU]

commit:     63026b2783c75a4f4d238a3731ed9c480ee51fbb
Author:     Benda Xu <heroxbd <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 24 08:10:01 2021 +0000
Commit:     Benda XU <heroxbd <AT> gentoo <DOT> org>
CommitDate: Sun Jan 24 08:10:45 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=63026b27

package.use.mask: mask sci-libs/pytorch[mkl].

Bug: https://github.com/gentoo/sci/issues/1011
Signed-off-by: Benda Xu <heroxbd <AT> gentoo.org>

 profiles/package.use.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 13ff264bb..3668ef20d 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -15,6 +15,11 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
+# Benda Xu <heroxbd@gentoo.org> (24 Jan 2021)
+# It doesn't work, mask 30 days for removal, unless someone come up
+# with a fix. cf. https://github.com/gentoo/sci/issues/1011
+sci-libs/pytorch mkl
+
 # Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
 # doesn't link with plotutils-2.6
 sci-physics/qcl plotutils

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

[Sam James]

commit:     c3e80e629a3c9289089ff1ed87de82aef269f4f6
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 12 21:43:54 2021 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Fri Feb 12 21:43:54 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c3e80e62

profiles/package.mask: mask Python 2-only packages

Signed-off-by: Sam James <sam <AT> gentoo.org>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..72e7e8c4b 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,9 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Sam James <sam@gentoo.org> (2021-02-12)
+# These versions need Python 2.7
+# Unspecified whether at build time (okay for now) or runtime (not)
+=sci-biology/canu-9999
+=sci-biology/Sibelia-9999

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

[Andrew Ammerlaan]

commit:     74dd0b3fd46cb3bda07033fda2eaf2c277c84c73
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Feb 13 11:30:56 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Feb 13 11:30:56 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=74dd0b3f

profiles/package.mask: mark sci-biology/Sibelia for removal in 14 days

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 07a777411..5124e1816 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,4 +33,9 @@
 # Sam James <sam@gentoo.org> (2021-02-12)
 # These versions need Python 2.7
 # Unspecified whether at build time (okay for now) or runtime (not)
+#
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (2021-02-13)
+# Checked the code, this is a **runtime** dependency. Upstream also
+# specifies this in their README file.
+# Removal in 14 days
 =sci-biology/Sibelia-9999

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

[Andrew Ammerlaan]

commit:     41f13097f28270c72d5e79f9025cfc52eef202cd
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar  4 14:21:07 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar  4 14:22:13 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=41f13097

package.mask: mask burrtools for removal

does not compile, last touched in 2015
last upstream update in 2013

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..c13674787 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,9 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (04 March 2021)
+# Burrtools does not compile, nor does the newest version (0.6.3)
+# The ebuild was last touched in 2015, last upstream update was in 2013
+# Masked for removal in 14 days, if you need this please complain
+sci-mathematics/burrtools

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

[Andrew Ammerlaan]

commit:     70cef5cec21b8621ecab62e939d3596cb98ff31b
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar  4 15:00:49 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar  4 15:00:49 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=70cef5ce

package.mask: mask libcgnsoo for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index c13674787..8ceae44de 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -35,3 +35,9 @@
 # The ebuild was last touched in 2015, last upstream update was in 2013
 # Masked for removal in 14 days, if you need this please complain
 sci-mathematics/burrtools
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (04 March 2021)
+# libcgnsoo does not compile, ebuild was last touched in 2015
+# no newer version available upstream
+# Masked for removal in 14 days, if you need this please complain
+sci-libs/libcgnsoo

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

[Andrew Ammerlaan]

commit:     51569a694bcfc4b6c593b06e6c6a13d342a9fa8e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar  5 08:34:31 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar  5 08:34:31 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=51569a69

package.mask: mask hydronmr for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 8ceae44de..f6b71c603 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -41,3 +41,8 @@ sci-mathematics/burrtools
 # no newer version available upstream
 # Masked for removal in 14 days, if you need this please complain
 sci-libs/libcgnsoo
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (05 March 2021)
+# Does not fetch, installs an exe, upstream website times out
+# Masked for removal in 14 days, if you need this please complain
+sci-chemistry/hydronmr

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

[Andrew Ammerlaan]

commit:     010e8d143669da03c0e7bc488633106a5c6e0923
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar  5 15:23:48 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar  5 15:29:12 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=010e8d14

package.mask: mask BG7 for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index f6b71c603..81a74bfc4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -46,3 +46,8 @@ sci-libs/libcgnsoo
 # Does not fetch, installs an exe, upstream website times out
 # Masked for removal in 14 days, if you need this please complain
 sci-chemistry/hydronmr
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (05 March 2021)
+# Does not build, live only, latest update 2013
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/BG7

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

[Andrew Ammerlaan]

commit:     863e61a89b6037ecaf8e66a8472a3b75ee930513
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar  5 21:49:28 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar  5 21:49:28 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=863e61a8

package.mask: mask autoeditor for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 81a74bfc4..021ccb507 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -51,3 +51,8 @@ sci-chemistry/hydronmr
 # Does not build, live only, latest update 2013
 # Masked for removal in 14 days, if you need this please complain
 sci-biology/BG7
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (05 March 2021)
+# Does not compile, last update in 2009
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/autoeditor

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

[Andrew Ammerlaan]

commit:     83dd738c9323fb92f03ae22e356bc9797f173dc5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 10:42:02 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 10:42:02 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=83dd738c

package.mask: mask dna2pep for removal, py2 only

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 021ccb507..dfffd5562 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -56,3 +56,9 @@ sci-biology/BG7
 # Does not compile, last update in 2009
 # Masked for removal in 14 days, if you need this please complain
 sci-biology/autoeditor
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (06 March 2021)
+# Python2 only
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/dna2pep
+

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

[Andrew Ammerlaan]

commit:     08649c8769259a20e69a18d9fe452c47aa3eb8a7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 10:51:33 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 10:51:33 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=08649c87

package.mask: mask edena for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index dfffd5562..818dab201 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -62,3 +62,7 @@ sci-biology/autoeditor
 # Masked for removal in 14 days, if you need this please complain
 sci-biology/dna2pep
 
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (06 March 2021)
+# Does not build, latest update 2013
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/edena

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

[Andrew Ammerlaan]

commit:     ff35287118feda145ac67fdf35a38dd3ba4266b5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 11:13:46 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 11:13:46 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ff352871

package.mask: mask grass for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 818dab201..2edf6ad2d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -66,3 +66,8 @@ sci-biology/dna2pep
 # Does not build, latest update 2013
 # Masked for removal in 14 days, if you need this please complain
 sci-biology/edena
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (06 March 2021)
+# missing dependency cplex (nonfree IBM thingy)
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/grass

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

[Andrew Ammerlaan]

commit:     da1e04623a37393bdaa4760388f120ca74bf3ed7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 11:28:21 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 11:28:21 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da1e0462

package.mask: mask igv for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 2edf6ad2d..b392b97e1 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -71,3 +71,10 @@ sci-biology/edena
 # missing dependency cplex (nonfree IBM thingy)
 # Masked for removal in 14 days, if you need this please complain
 sci-biology/grass
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (06 March 2021)
+# Newer versions use gradle build system which is currently not
+# support by portage, old versions do not build, ebuilds don't
+# have any keywords
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/igv

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

[Andrew Ammerlaan]

commit:     5bf849eafbfdb35cab3ef1d81267c9ca8419e64f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 13:21:15 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 13:21:15 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5bf849ea

package.mask: mask perga for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index b392b97e1..044d7b6b0 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -78,3 +78,8 @@ sci-biology/grass
 # have any keywords
 # Masked for removal in 14 days, if you need this please complain
 sci-biology/igv
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (06 March 2021)
+# Does not compile, latest update in 2015
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/perga

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

[Andrew Ammerlaan]

commit:     645af35a5d9f2dc27e70e6d9352f9ef24144c764
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 13:58:48 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 13:58:48 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=645af35a

package.mask: mask sclust for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 044d7b6b0..f21b1f315 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -83,3 +83,8 @@ sci-biology/igv
 # Does not compile, latest update in 2015
 # Masked for removal in 14 days, if you need this please complain
 sci-biology/perga
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (06 March 2021)
+# Does not fetch, last update in 2009
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/sclust

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

[Andrew Ammerlaan]

commit:     b223970e70e9b3dcefc68d03b87c3574f94e3fe8
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 15:00:53 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 15:00:53 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b223970e

package.mask: mask tclust for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index f21b1f315..6eb7f487c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -88,3 +88,8 @@ sci-biology/perga
 # Does not fetch, last update in 2009
 # Masked for removal in 14 days, if you need this please complain
 sci-biology/sclust
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (06 March 2021)
+# Does not build, last updated in 2009
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/tclust

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

[Andrew Ammerlaan]

commit:     e1a62e67726136b104f487dd53a82c040f56225e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 15:48:18 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 15:48:18 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1a62e67

package.mask: mask trowel for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 6eb7f487c..823764d0f 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -93,3 +93,9 @@ sci-biology/sclust
 # Does not build, last updated in 2009
 # Masked for removal in 14 days, if you need this please complain
 sci-biology/tclust
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (06 March 2021)
+# Does not compile with newer boost versions because endian.hpp
+# was removed.
+# Masked for removal in 14 days, if you need this please complain
+sci-biology/trowel

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

[Andrew Ammerlaan]

commit:     3aa070bd33026d3d9e7422e58ae60d3611676d66
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat May  8 12:56:31 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat May  8 12:56:31 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3aa070bd

profiles/package.mask: mask dev-java/netcdf for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/package.mask | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..fb07f4d8a 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,13 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@riseup.net> (08 May 2021)
+# netcdf(-java) is horribly outdated, it requires dev-java/ehcache which is
+# being removed. This ebuild cannot be moved into ::sci because the sources
+# are no longer available outside of the Gentoo mirror. Newer versions of
+# netcdf-java and ehcache use a maven based build system which currently does
+# not work with portage. The only real solution would be to add a netcdf-bin
+# package. If you need this software please complain on bugzilla or GitHub.
+# Masked for removal when dev-java/ehcache is removed from ::gentoo (~30 days).
+dev-java/netcdf

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

[Andrew Ammerlaan]

commit:     79d407ad9f2677b412a0fac076c47b95d0e4cd69
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon May 24 09:16:43 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon May 24 09:16:43 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=79d407ad

profiles/package.mask: mask dkms for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1dc69295f..db4ee576c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -39,3 +39,12 @@
 # package. If you need this software please complain on bugzilla or GitHub.
 # Masked for removal when dev-java/ehcache is removed from ::gentoo (~30 days).
 dev-java/netcdf
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (24 May 2021)
+# This was originally added for the NationalInstruments/GPIB ebuilds, however
+# due to the number of ebuilds it was decided to maintain these in ::natinst.
+# An ebuild for dkms was also added to ::natinst, so it makes little sense to
+# maintain an ebuild in ::sci as well. Additionally there is also an ebuild
+# for this in ::guru
+# Removal in 30 days
+sys-kernel/dkms

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

[Andrew Ammerlaan]

commit:     47f9d1da11c1f1f89975f24cc4e985a4d3c4cb3e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon Aug  2 13:21:51 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Aug  2 13:21:51 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=47f9d1da

profiles/package.mask: mask revdeps of ncbi-tools

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..5824044d1 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,16 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (02 Aug 2021)
+# These packages depend on ncbi-tools which is being removed from ::gentoo:
+# Last release 10 years ago, EOL upstream, no other distro packages this
+# anymore, tons of bugs. Revdeps are unmaintained too and out of date.
+# Bug #798015, removal in 30 days.
+# Perhaps these packages work with the newer ncbi-tools++? If anyone is actively
+# using these packages please open a bug report
+sci-biology/cg-cat
+sci-biology/cgview-bin
+sci-biology/prot4EST
+sci-biology/seqclean
+sci-chemistry/talosn

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

[Andrew Ammerlaan]

commit:     23f0365f2a9a95c8b482d4c037d7293b13b69477
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon Aug  2 13:25:59 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Aug  2 13:25:59 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=23f0365f

profiles/package.mask: more ncbi-tools revdep masks

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 5824044d1..8916d3ac2 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -42,3 +42,5 @@ sci-biology/cgview-bin
 sci-biology/prot4EST
 sci-biology/seqclean
 sci-chemistry/talosn
+# revdep of seqclean
+sci-biology/rum

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

[Andrew Ammerlaan]

commit:     a30c84d5f32898dafdd9d72ac4acd7dc3029ab8c
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Nov  4 09:01:31 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Nov  4 09:08:17 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a30c84d5

profiles/package.mask: mask sci-libs/geom for removal

Bug: https://github.com/gentoo/sci/issues/1119

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..a01fccbca 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,13 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (04 Nov 2021)
+# No upstream activity since 2011, does not build with sci-libs/opencascade:7.5.
+# Note that this package is NOT the salome geometry module but a standalone
+# version of that module that now appears to be abandoned. Packaging the
+# original salome geometry module requires packaging the salome kernel and the
+# salome gui module.
+# Masked for removal in 30 days or whenever sci-libs/opencascade:7.4.0:::gentoo
+# is removed.
+sci-libs/geom

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

[Andrew Ammerlaan]

commit:     6439a0a6bf53f99d37ffd4e71e00cfda062d2654
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 26 10:37:14 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Dec 26 10:38:25 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6439a0a6

package.mask: mask revdeps of cuda-10 for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..b1561a9ac 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,10 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Dec 2021)
+# cuda-10 is being removed from ::gentoo, mask revdeps in ::sci
+# for removal too. Removal in 90 days
+sci-physics/opticks
+sci-chemistry/MotionCor2
+

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

[Andrew Ammerlaan]

commit:     663249d5cd32e04a40cfa97104cd122d78703211
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 11 19:20:11 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 11 19:20:11 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=663249d5

profiles/package.mask: mask scilab and friends for removal

Use scilab-bin instead

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index b1561a9ac..d3d18176e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -36,3 +36,23 @@
 sci-physics/opticks
 sci-chemistry/MotionCor2
 
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org (11 Jan 2022)
+# Last-rite scilab in favour of scilab-bin. Scilab's java dependencies make
+# a from-source ebuild very difficult since portage doesn't support gradle or
+# maven. In addition it requires old versions of libraries that have already
+# been removed.
+# Removal in 30 days
+sci-mathematics/scilab
+>dev-java/lucene-4
+dev-java/flexdock
+dev-java/gluegen
+dev-java/jogl
+dev-java/jlatexmath
+dev-java/jlatexmath-fop
+dev-java/jfreechart
+dev-java/jfreesvg
+dev-java/jgraphx
+dev-java/jcommon
+dev-java/skinlf
+dev-java/jrosetta
+dev-java/freehep-graphicsio-emf

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

[Andrew Ammerlaan]

commit:     4726904c820b3c4b0977197aafaba5a1361182b9
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 11 19:23:52 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 11 19:23:52 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4726904c

profiles/package.mask: mask sci-biology/conrad for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d3d18176e..1721e4aca 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -56,3 +56,5 @@ dev-java/jcommon
 dev-java/skinlf
 dev-java/jrosetta
 dev-java/freehep-graphicsio-emf
+# and also mask this which hasn't seen an upstream release since 2007!
+sci-biology/conrad

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

[Andrew Ammerlaan]

commit:     ccd3711ad09044f68b18e0f72fe3c193ed472831
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 11 19:36:18 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 11 19:36:18 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ccd3711a

package.mask: mask sci-misc/europa-bin for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1721e4aca..4ac2f8a95 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -58,3 +58,7 @@ dev-java/jrosetta
 dev-java/freehep-graphicsio-emf
 # and also mask this which hasn't seen an upstream release since 2007!
 sci-biology/conrad
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org (11 Jan 2022)
+# Removal in 30 days, use jupyterlab-desktop instead.
+sci-misc/europa-bin

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

[Andrew Ammerlaan]

commit:     3897eb42a444bea12ba5c954b974f474c4e89846
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 13 15:15:50 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 13 15:15:50 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3897eb42

package.mask: mask jhdf5 for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 4ac2f8a95..63ccdbfb5 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -58,6 +58,8 @@ dev-java/jrosetta
 dev-java/freehep-graphicsio-emf
 # and also mask this which hasn't seen an upstream release since 2007!
 sci-biology/conrad
+# depends on dev-java/args4j which is being last-rited from ::gentoo
+sci-libs/jhdf5
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org (11 Jan 2022)
 # Removal in 30 days, use jupyterlab-desktop instead.

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

[Andrew Ammerlaan]

commit:     aaec9e65494575293b7e816c08540ca06d062115
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 13 15:24:13 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 13 15:24:13 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=aaec9e65

package.use.mask: drop obsolete use mask

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.use.mask | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 3668ef20d..13ff264bb 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -15,11 +15,6 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
-# Benda Xu <heroxbd@gentoo.org> (24 Jan 2021)
-# It doesn't work, mask 30 days for removal, unless someone come up
-# with a fix. cf. https://github.com/gentoo/sci/issues/1011
-sci-libs/pytorch mkl
-
 # Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
 # doesn't link with plotutils-2.6
 sci-physics/qcl plotutils

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

[Andrew Ammerlaan]

commit:     1a7f60be1e3372c066797beac859021a2282d013
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 13 15:46:52 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 13 15:46:52 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a7f60be

package.mask: mask htsjdk for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 63ccdbfb5..d67bd8056 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -60,6 +60,10 @@ dev-java/freehep-graphicsio-emf
 sci-biology/conrad
 # depends on dev-java/args4j which is being last-rited from ::gentoo
 sci-libs/jhdf5
+# ancient java, can't update due to gradle/maven limitation
+dev-java/htsjdk
+sci-biology/cramtools
+sci-biology/pilon-bin
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org (11 Jan 2022)
 # Removal in 30 days, use jupyterlab-desktop instead.

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

[Andrew Ammerlaan]

commit:     cf53c7003709db2c588a46db1195b3a55c3872a7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 13 15:50:28 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 13 15:50:28 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cf53c700

package.mask: mask terra for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d67bd8056..dd0cb7d5c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -65,6 +65,11 @@ dev-java/htsjdk
 sci-biology/cramtools
 sci-biology/pilon-bin
 
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org (13 Jan 2022)
+# Broken, no consumers
+# Removal in 30 days
+dev-lang/terra
+
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org (11 Jan 2022)
 # Removal in 30 days, use jupyterlab-desktop instead.
 sci-misc/europa-bin

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

[Andrew Ammerlaan]

commit:     88587a13f6f13736d25c31bf6cf260f51b9bf16d
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 14 10:13:56 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Jan 14 10:13:56 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=88587a13

package.mask: mask quorum for removal

Closes: https://github.com/gentoo/sci/issues/833

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index dd0cb7d5c..3107e5030 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -73,3 +73,10 @@ dev-lang/terra
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org (11 Jan 2022)
 # Removal in 30 days, use jupyterlab-desktop instead.
 sci-misc/europa-bin
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org (14 Jan 2022)
+# Does not compile, no upstream activity since 2016
+# https://github.com/gmarcais/Quorum/issues/2
+# https://github.com/gmarcais/Quorum/issues/1
+# Removal in 30 days
+sci-biology/quorum

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

[Andrew Ammerlaan]

commit:     03f1c71db6066efd9c47237b96aedfa11cdecff2
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 11:58:16 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 11:58:16 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=03f1c71d

package.mask: mask jigsaw for removal

Closes: https://github.com/gentoo/sci/issues/1071

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3107e5030..4583876b4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -80,3 +80,8 @@ sci-misc/europa-bin
 # https://github.com/gmarcais/Quorum/issues/1
 # Removal in 30 days
 sci-biology/quorum
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org (15 Jan 2022)
+# No updates since 2009(!), no longer compiles
+# Removal in 30 days
+sci-biology/jigsaw

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

[Andrew Ammerlaan]

commit:     9dfb78c05aaa8ff9edc2c795c2aac8692d3ed944
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 14:09:41 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 14:09:41 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9dfb78c0

package.use.mask: mask R and go flags on mlpack

Closes: https://github.com/gentoo/sci/issues/1084
Closes: https://github.com/gentoo/sci/issues/1085

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.use.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 13ff264bb..92d1d843a 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -26,3 +26,9 @@ sci-biology/estscan icc ifc
 # Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
 # gui sandbox error
 dev-lang/conceptual gui
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 Jan 2022)
+# dependencies not available
+# https://github.com/gentoo/sci/issues/1085
+# https://github.com/gentoo/sci/issues/1084
+sci-libs/mlpack go R

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

[Andrew Ammerlaan]

commit:     3a82e2bee5be713c92ad86e6f4bec8d297fa472b
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 16 09:51:57 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Jan 16 09:51:57 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a82e2be

package.mask: mask opennlp-maxent for removal

depends on dev-java/trove which is being removed from ::gentoo

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 4583876b4..672cc7b74 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -64,6 +64,7 @@ sci-libs/jhdf5
 dev-java/htsjdk
 sci-biology/cramtools
 sci-biology/pilon-bin
+sci-misc/opennlp-maxent
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org (13 Jan 2022)
 # Broken, no consumers

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

[Andrew Ammerlaan]

commit:     10134bf04fc57433391c27830f2da6c91460f0f2
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 21 14:09:42 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Jan 21 14:09:42 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=10134bf0

package.mask: mask jtreeview for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 672cc7b74..a1c408aaf 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -86,3 +86,7 @@ sci-biology/quorum
 # No updates since 2009(!), no longer compiles
 # Removal in 30 days
 sci-biology/jigsaw
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org (21 Jan 2022)
+# Requires dev-java/nanoxml which is masked for removal in ::gentoo
+sci-biology/jtreeview

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

[Andrew Ammerlaan]

commit:     1ddc16c78ccae513b383e39f2556c3afadf25613
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 15 19:12:15 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Mar 15 19:12:15 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ddc16c7

package.mask: mask superlu_dist for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..effdccc93 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,8 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 Mar 2022)
+# Missing dependencies, bumping is non-trivial, requires patches to get it to
+# compile without errors or sandbox violations. Mask for removal, no revdeps
+sci-libs/superlu_dist

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

[Andrew Ammerlaan]

commit:     9136a0e12311f8f0220a6fb09195398cb1b0f93f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sun May 15 12:28:23 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun May 15 12:30:55 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9136a0e1

profiles/package.mask: mask jeuclid-core for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..b338c8d20 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,9 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 May 2022)
+# Requires old and removed batik:1.9::gentoo
+# No updates since 2019
+# Mask for removal in 30 days
+dev-java/jeuclid-core

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

[Andrew Ammerlaan]

commit:     67bbcb562b65f49f3d32f5aaa2ed9b54c6c25071
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 20 09:44:35 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Jul 20 09:44:35 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=67bbcb56

profiles: mask dev-python/llvmlite for removal

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..18b8386b7 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,8 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (20 Jul 2022)
+# Depends on removed llvm:12
+# removal in 30 days
+dev-python/llvmlite

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

[Andrew Ammerlaan]

commit:     52eabadff644fd21f6a66671a493efcef3bac059
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 20 09:49:36 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Jul 20 09:49:57 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=52eabadf

profiles: mask revdeps of llvmlite

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 18b8386b7..97229a503 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,3 +34,6 @@
 # Depends on removed llvm:12
 # removal in 30 days
 dev-python/llvmlite
+# reverse dependencies of llvmlite
+dev-python/numba
+dev-python/pynndescent

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

[Andrew Ammerlaan]

commit:     2c4dd4f6d3ce90943deb1e7c35caeb5fd70b0674
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 20 09:55:03 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Jul 20 09:55:03 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2c4dd4f6

profiles: mask dev-python/umap-learn

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 97229a503..e7a18b54f 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -37,3 +37,5 @@ dev-python/llvmlite
 # reverse dependencies of llvmlite
 dev-python/numba
 dev-python/pynndescent
+# reverse dependencies of numba
+dev-python/umap-learn

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

[Andrew Ammerlaan]

commit:     0207d357e76c949c828c97a8013a2eb7384705c9
Author:     Yiyang Wu <xgreenlandforwyy <AT> gmail <DOT> com>
AuthorDate: Thu Aug  4 09:30:01 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Aug  7 08:40:44 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0207d357

profiles: unmask dev-python/{numba,llvmlite}

The newset version can depend on llvm:13 which is still in ::gentoo

And there is ongoing efforts of migrating to llvm:14
See https://github.com/numba/llvmlite/pull/830

Signed-off-by: Yiyang Wu <xgreenlandforwyy <AT> gmail.com>
Closes: https://github.com/gentoo/sci/pull/1164
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index e7a18b54f..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,13 +29,3 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (20 Jul 2022)
-# Depends on removed llvm:12
-# removal in 30 days
-dev-python/llvmlite
-# reverse dependencies of llvmlite
-dev-python/numba
-dev-python/pynndescent
-# reverse dependencies of numba
-dev-python/umap-learn

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

[Andrew Ammerlaan]

commit:     bb8f8e9511ac3c146629af13822d6d18e8d295ea
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 22 15:12:21 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Aug 22 15:12:21 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bb8f8e95

profiles: mask revdeps of sci-libs/io_lib

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..a635ec62c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,10 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2022-08-22)
+# Depends on removed sci-libs/io_lib. removal in 30 days
+sci-biology/caftools
+sci-biology/salmon
+sci-biology/staden
+sci-biology/staden_doc

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

[Andrew Ammerlaan]

commit:     df2784cdca02e3bf9ad4ace128474dd7495676c5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 22 15:14:48 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Aug 22 15:14:48 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=df2784cd

profiles: mask more revdeps

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index a635ec62c..a21bb9773 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -36,3 +36,4 @@ sci-biology/caftools
 sci-biology/salmon
 sci-biology/staden
 sci-biology/staden_doc
+sci-biology/roche454ace2caf

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

[Andrew Ammerlaan]

commit:     c148e18f7f7b17200ec761f7d2afbe758c5ab72c
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 23 08:06:31 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 23 10:58:13 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c148e18f

profiles: mask gdcm[python] depends on non-existent vtk version

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.use.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 92d1d843a..508ab17db 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -15,6 +15,10 @@
 ## =media-video/mplayer-0.90_pre5-r1 foo
 #
 
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (23 Aug 2022)
+# vtk<9 no longer available in ::gentoo
+sci-libs/gdcm python
+
 # Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
 # doesn't link with plotutils-2.6
 sci-physics/qcl plotutils

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

[Andrew Ammerlaan]

commit:     d3d63c165da3d4f3782ef06f718996126f68b8f6
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  1 21:56:43 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Dec  1 21:56:43 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d3d63c16

profiles: cleanup entry for non-existent package

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.use.mask | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index b4116bd86..79c0fcb5c 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -19,10 +19,6 @@
 # vtk<9 no longer available in ::gentoo
 sci-libs/gdcm python
 
-# Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
-# doesn't link with plotutils-2.6
-sci-physics/qcl plotutils
-
 # Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
 # gui sandbox error
 dev-lang/conceptual gui

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

[Andrew Ammerlaan]

commit:     986193d5c7ae9b79963c5320b5362115aef88c06
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 12 11:57:32 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 12 11:59:01 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=986193d5

profiles: mask packages that need bump to py3.10+

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..69343d5b7 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,30 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
+# Needs bump of PYTHON_COMPAT to at least python3_10
+sci-biology/tigmint
+sci-biology/nitime
+sci-biology/deeptools
+sci-biology/gemini
+sci-biology/gffutils
+sci-biology/chiron
+dev-python/snakemake
+dev-python/pyvista
+dev-python/specutils
+dev-python/regions
+dev-python/pyzo
+dev-python/persim
+dev-python/panel
+dev-python/kmapper
+dev-python/photutils
+dev-python/gwcs
+dev-python/gammapy
+dev-python/asdf
+dev-python/astroquery
+# Reverse deps of above
+dev-python/holoviews
+dev-python/ripser
+sci-biology/arcs
+sci-biology/longstitch

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

[Andrew Ammerlaan]

commit:     2fb7b4e4079686b89ca696ac7837cfcb10c26695
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 12 12:16:05 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 12 12:16:05 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2fb7b4e4

profiles: mask packages still depending on nose

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 69343d5b7..bccc7a16d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -56,3 +56,17 @@ dev-python/holoviews
 dev-python/ripser
 sci-biology/arcs
 sci-biology/longstitch
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
+# Depends on dev-python/nose, needs porting to pytest
+sci-libs/nipy
+sci-biology/pyfaidx
+sci-biology/gffutils
+sci-biology/RSeQC
+sci-biology/Fastaq
+sci-biology/deeptools
+dev-python/traits
+dev-python/hdf5storage
+dev-python/transforms3d
+dev-python/annexremote
+dev-python/pysolar

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

[Andrew Ammerlaan]

commit:     dae6ebe82dfe6f98de3238d98066b00a5d4d6a66
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 12 12:17:40 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 12 12:17:40 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dae6ebe8

profiles: mask packages still depending on nose

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index bccc7a16d..50b538443 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -70,3 +70,5 @@ dev-python/hdf5storage
 dev-python/transforms3d
 dev-python/annexremote
 dev-python/pysolar
+# Reverse deps of above
+dev-vcs/datalad

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

[Andrew Ammerlaan]

commit:     f6063ad6adbbfd4386ac163670b6c7bf91692927
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 12 12:20:42 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 12 12:20:42 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f6063ad6

profiles: mask more revdeps

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 50b538443..dc9da2ce5 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -72,3 +72,5 @@ dev-python/annexremote
 dev-python/pysolar
 # Reverse deps of above
 dev-vcs/datalad
+sci-biology/samri
+sci-libs/nipype

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

[Horea Christian]

commit:     9360858627cb06129382d31f5d49e935d0c816dd
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jan 12 22:18:38 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 12 22:18:38 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=93608586

profiles: is test restricted

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index dc9da2ce5..922b70f3e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -59,7 +59,6 @@ sci-biology/longstitch
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Depends on dev-python/nose, needs porting to pytest
-sci-libs/nipy
 sci-biology/pyfaidx
 sci-biology/gffutils
 sci-biology/RSeQC

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

[Horea Christian]

commit:     58d24cfc469084887cb5e65346cfbe2dc0741fdb
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jan 12 23:51:43 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 12 23:51:43 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=58d24cfc

profiles: no error for package

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 922b70f3e..9798c0df7 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -64,7 +64,6 @@ sci-biology/gffutils
 sci-biology/RSeQC
 sci-biology/Fastaq
 sci-biology/deeptools
-dev-python/traits
 dev-python/hdf5storage
 dev-python/transforms3d
 dev-python/annexremote

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

[Horea Christian]

commit:     a55baa11cf375d05f43d38042b9078a7e7aac8b5
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 06:20:37 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 06:20:37 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a55baa11

profiles: dev-python/annexremote causes no errors

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9798c0df7..cd56346bf 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -66,7 +66,6 @@ sci-biology/Fastaq
 sci-biology/deeptools
 dev-python/hdf5storage
 dev-python/transforms3d
-dev-python/annexremote
 dev-python/pysolar
 # Reverse deps of above
 dev-vcs/datalad

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

[Horea Christian]

commit:     cfadcb30f5f733326cf70fba3b39ddad24f10a17
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 07:00:49 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 07:00:49 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cfadcb30

profiles: sci-biology/nitime python compatibility fixed

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index cd56346bf..3d1ba947e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,7 +33,6 @@
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Needs bump of PYTHON_COMPAT to at least python3_10
 sci-biology/tigmint
-sci-biology/nitime
 sci-biology/deeptools
 sci-biology/gemini
 sci-biology/gffutils

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

[Horea Christian]

commit:     a13cad7fa16533ca21e20bb7f39642602896f618
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 07:03:21 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 07:03:21 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a13cad7f

profiles: dependencies unmasked

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3d1ba947e..32408cfdf 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -66,7 +66,3 @@ sci-biology/deeptools
 dev-python/hdf5storage
 dev-python/transforms3d
 dev-python/pysolar
-# Reverse deps of above
-dev-vcs/datalad
-sci-biology/samri
-sci-libs/nipype

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

[Horea Christian]

commit:     e2726eb31b1c3644ddee6168fa5f77bae5b10693
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 07:42:46 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 07:42:46 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e2726eb3

profiles: sci-biology/tigmint PYTHON_COMPAT updated

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 32408cfdf..d67ffb203 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -32,7 +32,6 @@
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Needs bump of PYTHON_COMPAT to at least python3_10
-sci-biology/tigmint
 sci-biology/deeptools
 sci-biology/gemini
 sci-biology/gffutils

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

[Horea Christian]

commit:     7e46d4bd9c621fcac1aabf1da862b5b770ce5ae7
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 08:58:47 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 08:58:47 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7e46d4bd

profiles: package no longer errors

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index d67ffb203..986f9acc7 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -32,7 +32,6 @@
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Needs bump of PYTHON_COMPAT to at least python3_10
-sci-biology/deeptools
 sci-biology/gemini
 sci-biology/gffutils
 sci-biology/chiron
@@ -61,7 +60,6 @@ sci-biology/pyfaidx
 sci-biology/gffutils
 sci-biology/RSeQC
 sci-biology/Fastaq
-sci-biology/deeptools
 dev-python/hdf5storage
 dev-python/transforms3d
 dev-python/pysolar

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

[Horea Christian]

commit:     a1b726e22a8ae9d77f915e75d0e39a99400a24a1
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 19:28:53 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 19:28:53 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1b726e2

profiles: fixed PYTHON_COMPAt

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 986f9acc7..cacd3491c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -32,7 +32,6 @@
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Needs bump of PYTHON_COMPAT to at least python3_10
-sci-biology/gemini
 sci-biology/gffutils
 sci-biology/chiron
 dev-python/snakemake

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

[Horea Christian]

commit:     84ed01ae78910b4424cd2270241720cea897e0b8
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 20:22:31 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 20:22:31 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=84ed01ae

profiles: gwcs updated

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index cacd3491c..b152090c5 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -43,7 +43,6 @@ dev-python/persim
 dev-python/panel
 dev-python/kmapper
 dev-python/photutils
-dev-python/gwcs
 dev-python/gammapy
 dev-python/asdf
 dev-python/astroquery

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

[Horea Christian]

commit:     2e3e22579110e476e1f549ba59f741612f778401
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 22:00:22 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 22:00:22 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e3e2257

profiles: dev-python/asdf issues solved

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index b152090c5..9d0e2fe50 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -44,7 +44,6 @@ dev-python/panel
 dev-python/kmapper
 dev-python/photutils
 dev-python/gammapy
-dev-python/asdf
 dev-python/astroquery
 # Reverse deps of above
 dev-python/holoviews

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

[Horea Christian]

commit:     e58e6b9d616219399fdb07940aac3b9b305beedf
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 23:34:17 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 23:34:17 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e58e6b9d

profiles: pyvista no longer breaks the depgraph

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9d0e2fe50..6a88b2fa9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -35,7 +35,6 @@
 sci-biology/gffutils
 sci-biology/chiron
 dev-python/snakemake
-dev-python/pyvista
 dev-python/specutils
 dev-python/regions
 dev-python/pyzo

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

[Horea Christian]

commit:     3a53d23ac91246de0d682d35b06030eaaf9dc043
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Jan 14 10:31:50 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Jan 14 10:31:50 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a53d23a

profiles: dev-python/persim no longer fails

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 6a88b2fa9..765ddcbc7 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,7 +38,6 @@ dev-python/snakemake
 dev-python/specutils
 dev-python/regions
 dev-python/pyzo
-dev-python/persim
 dev-python/panel
 dev-python/kmapper
 dev-python/photutils

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

[Horea Christian]

commit:     6ed21e5b1191124b2119e83f1e32d44394b5a195
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Jan 14 11:51:40 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Jan 14 11:51:40 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ed21e5b

profiles: sci-biology/Fastaq issues solved

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 765ddcbc7..1942944f6 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -54,7 +54,6 @@ sci-biology/longstitch
 sci-biology/pyfaidx
 sci-biology/gffutils
 sci-biology/RSeQC
-sci-biology/Fastaq
 dev-python/hdf5storage
 dev-python/transforms3d
 dev-python/pysolar

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

[Horea Christian]

commit:     1ec270f5e4257488b39886e0ade87563a0fcecde
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Jan 15 17:51:34 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Jan 15 17:51:34 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ec270f5

profiles: py3.10 available for holoviews stack

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1942944f6..3f6a655f3 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,13 +38,11 @@ dev-python/snakemake
 dev-python/specutils
 dev-python/regions
 dev-python/pyzo
-dev-python/panel
 dev-python/kmapper
 dev-python/photutils
 dev-python/gammapy
 dev-python/astroquery
 # Reverse deps of above
-dev-python/holoviews
 dev-python/ripser
 sci-biology/arcs
 sci-biology/longstitch

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

[Horea Christian]

commit:     3eb1934fb17a153026d22daa9a53a41aa104cde8
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Jan 15 20:23:54 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Jan 15 20:23:54 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3eb1934f

profiles: sci-biology/arcs dep stack cleared

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3f6a655f3..ef1fd73f3 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -44,7 +44,6 @@ dev-python/gammapy
 dev-python/astroquery
 # Reverse deps of above
 dev-python/ripser
-sci-biology/arcs
 sci-biology/longstitch
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)

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

[Horea Christian]

commit:     78b2c0f8dd5b888739b7a97003efe103a3524d02
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 16 00:46:13 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 16 00:46:13 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=78b2c0f8

profiles: sci-biology/longstitch dep stack cleared

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index ef1fd73f3..a0d859d7f 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -44,7 +44,6 @@ dev-python/gammapy
 dev-python/astroquery
 # Reverse deps of above
 dev-python/ripser
-sci-biology/longstitch
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Depends on dev-python/nose, needs porting to pytest

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

[Andrew Ammerlaan]

commit:     dc733d93060b7b01c10867bbc02c4208d7d79ff0
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 10 13:29:32 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Feb 10 13:29:32 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc733d93

profiles: mask sci-biology/trans-abyss

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 1 +
 1 file changed, 1 insertion(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 0596e0782..25e3558f8 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,6 +34,7 @@
 # Needs bump of PYTHON_COMPAT to at least python3_10
 sci-biology/gffutils
 sci-biology/chiron
+sci-biology/trans-abyss
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Depends on dev-python/nose, needs porting to pytest

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

[Andrew Ammerlaan]

commit:     ead757b56b3a7e38e95251371cb4206eace80626
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 10 13:35:52 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Feb 10 13:35:52 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ead757b5

profiles: mask packages with missing checksums

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 25e3558f8..188bab233 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -41,3 +41,12 @@ sci-biology/trans-abyss
 sci-biology/pyfaidx
 sci-biology/gffutils
 sci-biology/RSeQC
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org) (10 Feb 2023)
+# Fetch restricted ebuilds without proper manifest entry
+dev-lang/pgi
+sci-biology/signalp
+sci-biology/tmhmm
+sci-chemistry/ligplot+
+sci-chemistry/nmrview
+sci-chemistry/rosetta-tools

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

[Andrew Ammerlaan]

commit:     0a40e11ac4f93df6cc97e53b24706c34863a04f9
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 17 14:02:57 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Mar 17 14:02:57 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a40e11a

profiles: mask sci-biology/ants

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 188bab233..f95f8e28c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,12 @@
 
 #--- END OF EXAMPLES ---
 
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (17 Mar 2023)
+# Needs bump to support vtk-9.2 (vtk-9.1 removed). This likely
+# requires bumping the version which would also require bumping
+# sci-libs/itk
+sci-biology/ants
+
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Needs bump of PYTHON_COMPAT to at least python3_10
 sci-biology/gffutils

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

[Andrew Ammerlaan]

commit:     da33e05fe0b36a64bc5b8524b65d6978135de844
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 17 14:06:32 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Mar 17 14:06:32 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da33e05f

profiles: also maks sci-biology/samri

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index f95f8e28c..37e5273d0 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -35,6 +35,8 @@
 # requires bumping the version which would also require bumping
 # sci-libs/itk
 sci-biology/ants
+# revdep of above
+sci-biology/samri
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Needs bump of PYTHON_COMPAT to at least python3_10

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

[Horea Christian]

commit:     d14ba1e4c57bcd0b12488eed12d82facb664c0bc
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 04:45:37 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 04:45:37 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d14ba1e4

profiles: packages issues addressed

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 37e5273d0..4c649adb9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -46,7 +46,6 @@ sci-biology/trans-abyss
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Depends on dev-python/nose, needs porting to pytest
-sci-biology/pyfaidx
 sci-biology/gffutils
 sci-biology/RSeQC
 

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

[Horea Christian]

commit:     10c79dc12eeb0e5052f7de8608bd34a78ab09f43
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 05:16:45 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 05:16:45 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=10c79dc1

profiles: package issues resolved

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 4c649adb9..147869ad2 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -40,13 +40,11 @@ sci-biology/samri
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Needs bump of PYTHON_COMPAT to at least python3_10
-sci-biology/gffutils
 sci-biology/chiron
 sci-biology/trans-abyss
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Depends on dev-python/nose, needs porting to pytest
-sci-biology/gffutils
 sci-biology/RSeQC
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (10 Feb 2023)

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

[Horea Christian]

commit:     1eafc176027de6359599c9d1e54bd0374891b7b0
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Mar 29 04:05:56 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Mar 29 04:08:02 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1eafc176

profiles: providing required dependencies

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 147869ad2..d6599c66f 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,7 +34,6 @@
 # Needs bump to support vtk-9.2 (vtk-9.1 removed). This likely
 # requires bumping the version which would also require bumping
 # sci-libs/itk
-sci-biology/ants
 # revdep of above
 sci-biology/samri
 

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

[Horea Christian]

commit:     ce13899e857dfed9f0f50a32819ae487ce659887
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Mar 29 05:04:36 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Mar 29 05:04:36 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ce13899e

profiles: providing full dependency stack

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index d6599c66f..80bd60014 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,13 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (17 Mar 2023)
-# Needs bump to support vtk-9.2 (vtk-9.1 removed). This likely
-# requires bumping the version which would also require bumping
-# sci-libs/itk
-# revdep of above
-sci-biology/samri
-
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org) (12 Jan 2023)
 # Needs bump of PYTHON_COMPAT to at least python3_10
 sci-biology/chiron

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

[Andrew Ammerlaan]

commit:     f63436394c638f7c5f002a692b7e45ebc949521a
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:35:12 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:35:12 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f6343639

profiles: cleanup old entries

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.use.mask | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 79c0fcb5c..39a6df0b7 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -18,7 +18,3 @@
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (23 Aug 2022)
 # vtk<9 no longer available in ::gentoo
 sci-libs/gdcm python
-
-# Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
-# gui sandbox error
-dev-lang/conceptual gui

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

[Andrew Ammerlaan]

commit:     8a77f2837b8cc397a0703983e7d6ea7f22305c47
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 26 17:54:19 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Jun 26 17:54:19 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a77f283

profiles: mask dev-python/cadquery*

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..9f3b8e7f5 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,10 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Jun 2023)
+# Depends on removed dev-python/toml.
+# Alternatives are tomli or tomlkit
+dev-python/cadquery
+dev-python/cadquery-ocp
+dev-python/cadquery-pywrap

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

[Andrew Ammerlaan]

commit:     1d7cb19d427b664d94b8c8db416b9820a8242090
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Oct 24 07:52:45 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Oct 24 07:52:45 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1d7cb19d

profiles: mask nptyping revdeps

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9f3b8e7f5..3aac93f31 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,11 @@
 
 #--- END OF EXAMPLES ---
 
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (24 Oct 2023)
+# Depends on removed dev-python/nptyping
+dev-python/pynrrd
+dev-python/typish
+
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Jun 2023)
 # Depends on removed dev-python/toml.
 # Alternatives are tomli or tomlkit

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

[Horea Christian]

commit:     6912b6bbc31088b709dbcfb775b60b5ef419a8a5
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Dec  1 15:04:29 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Dec  1 15:04:29 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6912b6bb

profiles: nptyping reinstated

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 3aac93f31..9f3b8e7f5 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,11 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (24 Oct 2023)
-# Depends on removed dev-python/nptyping
-dev-python/pynrrd
-dev-python/typish
-
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Jun 2023)
 # Depends on removed dev-python/toml.
 # Alternatives are tomli or tomlkit

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

[Andrew Ammerlaan]

commit:     c79afc63534d2ba48f22fb857c4139d10d400fab
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 18 15:33:12 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Dec 18 15:33:12 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c79afc63

profiles: mask sci-libs/nipype

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9f3b8e7f5..b51a8ddcc 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,12 @@
 
 #--- END OF EXAMPLES ---
 
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (16 Dec 2023)
+# Depends on removed dev-python/pydotplus
+sci-libs/nipype
+dev-python/heudiconv
+sci-biology/samri
+
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Jun 2023)
 # Depends on removed dev-python/toml.
 # Alternatives are tomli or tomlkit

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

[Andrew Ammerlaan]

commit:     4495bb4fb18a789d54ccacea7f9bf1973f846ef8
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 29 09:54:40 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Dec 29 09:54:40 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4495bb4f

profiles: mask llvmlite

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index b51a8ddcc..1bcec67dc 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,13 @@
 
 #--- END OF EXAMPLES ---
 
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (29 Dec 2023)
+# Depends on removed llvm:14, at the time of writing no llvm:15
+# update available.
+dev-python/llvmlite
+dev-python/numba
+dev-python/numba-dpex
+
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (16 Dec 2023)
 # Depends on removed dev-python/pydotplus
 sci-libs/nipype

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

[Andrew Ammerlaan]

commit:     88304a8f232c2d6576e174655b05bfa66d605621
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 29 10:05:25 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Dec 29 10:05:25 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=88304a8f

profiles: mask reverse deps of numba

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1bcec67dc..78a8b2480 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -36,6 +36,10 @@
 dev-python/llvmlite
 dev-python/numba
 dev-python/numba-dpex
+dev-python/pynndescent
+# Reverse dep of numba
+dev-python/tridesclous
+dev-python/umap-learn
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (16 Dec 2023)
 # Depends on removed dev-python/pydotplus

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

[Horea Christian]

commit:     5c3158f9fbd0a76cfea2663ffbb197baf371e864
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 14:39:39 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 14:39:39 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5c3158f9

profiles: removed old package version with dropped dependency

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 78a8b2480..56bf41059 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -43,7 +43,6 @@ dev-python/umap-learn
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (16 Dec 2023)
 # Depends on removed dev-python/pydotplus
-sci-libs/nipype
 dev-python/heudiconv
 sci-biology/samri
 

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

[Horea Christian]

commit:     41349a88222444a77180a5b55e43c1d5a2ec92d7
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 14:41:36 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 14:41:36 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=41349a88

profiles: heudiconv package no longer affected by dropped dependency

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 60e453d16..527c834e4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -41,10 +41,6 @@ dev-python/pynndescent
 dev-python/tridesclous
 dev-python/umap-learn
 
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (16 Dec 2023)
-# Depends on removed dev-python/pydotplus
-dev-python/heudiconv
-
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Jun 2023)
 # Depends on removed dev-python/toml.
 # Alternatives are tomli or tomlkit

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

[Horea Christian]

commit:     f9d3a76bb758353dcb4eefd37bd8159c5b369eb7
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 14:40:35 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 14:40:35 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9d3a76b

profiles: samri package no longer affected by deprecated dependency

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 1 -
 1 file changed, 1 deletion(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 56bf41059..60e453d16 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -44,7 +44,6 @@ dev-python/umap-learn
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (16 Dec 2023)
 # Depends on removed dev-python/pydotplus
 dev-python/heudiconv
-sci-biology/samri
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (26 Jun 2023)
 # Depends on removed dev-python/toml.

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

[Andrew Ammerlaan]

commit:     392b8a17389643a9f9b5b467b0c0aacb11c1f38a
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 27 14:40:14 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Feb 27 14:40:14 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=392b8a17

profiles: mask dev-python/pytorch-lightning

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 527c834e4..adc653878 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,10 @@
 
 #--- END OF EXAMPLES ---
 
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (27-02-2024)
+# Depends on removed sci-visualization/tensorboard
+dev-python/pytorch-lightning
+
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (29 Dec 2023)
 # Depends on removed llvm:14, at the time of writing no llvm:15
 # update available.

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

[Andrew Ammerlaan]

commit:     557d3b57a23fc54c993f0296b1935a06bc99bf8e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 15 11:25:41 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Mar 15 11:25:41 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=557d3b57

mask packs with incomp deps

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..9384fafc7 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,11 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-03-15)
+# Depends on removed dev-python/pydantic
+dev-python/dandi-schema
+dev-vcs/dandi-cli
+sci-biology/neuroconv
+# Depends on unkeyworded dev-libs/libpthread-stubs
+sci-biology/afni

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

[Andrew Ammerlaan]

commit:     481cfc5b24936c3b6d9216861e6a438a8db9c7c6
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 15 11:28:27 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Mar 15 11:28:27 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=481cfc5b

mask packs with incomp deps

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index 9384fafc7..b908c0a3e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -37,3 +37,6 @@ dev-vcs/dandi-cli
 sci-biology/neuroconv
 # Depends on unkeyworded dev-libs/libpthread-stubs
 sci-biology/afni
+sci-biology/samri
+sci-biology/samri_bidsdata
+sci-biology/samri_bindata

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

[Horea Christian]

commit:     b846f5dfcb198edc40f2061b2e8bbf2cd3f555ad
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Mar 21 22:11:32 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Mar 21 22:15:29 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b846f5df

profiles: unmasked packages with formerly missing deps

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index b908c0a3e..464a4005a 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -31,10 +31,6 @@
 #--- END OF EXAMPLES ---
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-03-15)
-# Depends on removed dev-python/pydantic
-dev-python/dandi-schema
-dev-vcs/dandi-cli
-sci-biology/neuroconv
 # Depends on unkeyworded dev-libs/libpthread-stubs
 sci-biology/afni
 sci-biology/samri

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

[Horea Christian]

commit:     e3c9b1be480b74fa4b9d1b84002f8a2d261c6163
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Mar 22 21:19:03 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Mar 22 21:19:03 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e3c9b1be

profiles: unmasked packages with formerly missing deps

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 464a4005a..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,10 +29,3 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-03-15)
-# Depends on unkeyworded dev-libs/libpthread-stubs
-sci-biology/afni
-sci-biology/samri
-sci-biology/samri_bidsdata
-sci-biology/samri_bindata

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

[Andrew Ammerlaan]

commit:     ca51d5147ba4ef27db118dffc07302eaac1bc7b9
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 24 09:34:43 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Apr 24 09:34:43 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca51d514

package.mask: mask multiqc and nipype

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index d39812beb..efc64be51 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,3 +29,16 @@
 ## app-misc/some-package
 
 #--- END OF EXAMPLES ---
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
+# Dependencies dev-python/future removed
+sci-biology/multiqc
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
+# Dependencies dev-python/prov removed
+sci-libs/nipype
+# reverse deps
+sci-biology/samri
+sci-biology/samri_bidsdata
+sci-biology/samri_bindata
+dev-python/heudiconv

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

[Horea Christian]

commit:     670b006885dabe96503628a52ddfc6d9a6635c57
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu May  9 22:51:59 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu May  9 22:51:59 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=670b0068

profiles: unmasked nipype

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 2 --
 1 file changed, 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index efc64be51..09429792d 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -35,8 +35,6 @@
 sci-biology/multiqc
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
-# Dependencies dev-python/prov removed
-sci-libs/nipype
 # reverse deps
 sci-biology/samri
 sci-biology/samri_bidsdata

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

[Horea Christian]

commit:     1b90823136a7aa189484deb0f3769daf58d3c040
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu May  9 23:02:28 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu May  9 23:02:28 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1b908231

profiles: unmasked samri, heudiconv

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 profiles/package.mask | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 09429792d..48068ccf9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -36,7 +36,3 @@ sci-biology/multiqc
 
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
 # reverse deps
-sci-biology/samri
-sci-biology/samri_bidsdata
-sci-biology/samri_bindata
-dev-python/heudiconv

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

[Andrew Ammerlaan]

commit:     633f65383dbc7bcc1178b2e2caeaa6929bb79c5b
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 18 11:28:40 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jul 18 11:28:40 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=633f6538

profiles: mask  sci-biology/BBmap

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1b622a85b..c184ca27b 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,5 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-04-24)
-# reverse deps
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-07-18)
+# Requires java openmpi bindings, no longer packaged.
+sci-biology/BBmap

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

[Andrew Ammerlaan]

commit:     62e0d7db6b9ad59da6294bfeb08187fd495ab2f2
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 30 08:29:46 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Oct 30 08:29:46 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=62e0d7db

profiles: mask ant-core revdeps

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/profiles/package.mask b/profiles/package.mask
index c184ca27b..03b10f53a 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,3 +33,10 @@
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-07-18)
 # Requires java openmpi bindings, no longer packaged.
 sci-biology/BBmap
+
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-10-30)
+# Requires removed dev-java/ant-core
+sci-biology/MeV
+sci-biology/SnpEff
+sci-biology/trimmomatic
+sci-biology/trinityrnaseq

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

[Alexander Puck Neuwirth]

commit:     ecf267755d717101cc11115f2b953ad573c56e29
Author:     Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de>
AuthorDate: Sat Nov  9 07:41:28 2024 +0000
Commit:     Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de>
CommitDate: Sat Nov  9 07:53:47 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ecf26775

profiles: unmask ant-core revdeps

Signed-off-by: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik.de>
Closes: https://github.com/gentoo/sci/pull/1294

 profiles/package.mask | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 03b10f53a..c184ca27b 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,10 +33,3 @@
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-07-18)
 # Requires java openmpi bindings, no longer packaged.
 sci-biology/BBmap
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-10-30)
-# Requires removed dev-java/ant-core
-sci-biology/MeV
-sci-biology/SnpEff
-sci-biology/trimmomatic
-sci-biology/trinityrnaseq