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commit: 3f7c507a97b62ef814517adf3e9fae935db4ad04 |
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Author: Benda Xu <heroxbd <AT> gentoo <DOT> org> |
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AuthorDate: Wed May 30 05:25:20 2018 +0000 |
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Commit: Benda XU <heroxbd <AT> gentoo <DOT> org> |
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CommitDate: Wed May 30 05:25:20 2018 +0000 |
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URL: https://gitweb.gentoo.org/proj/R_overlay.git/commit/?id=3f7c507a |
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|
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Use regex in dep string matches. |
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|
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Ignore rules should come later than positive rules. |
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|
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Closes: https://bugs.gentoo.org/653694 |
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|
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config/simple-deprules.d/R | 66 ++++++------ |
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config/simple-deprules.d/app | 7 +- |
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config/simple-deprules.d/app-text | 29 +----- |
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config/simple-deprules.d/compound_deps | 25 ++--- |
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config/simple-deprules.d/dev | 58 ++--------- |
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config/simple-deprules.d/dev-libs | 73 +++----------- |
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config/simple-deprules.d/dot_remap | 134 ------------------------- |
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config/simple-deprules.d/ignored_text | 103 ++++++------------- |
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config/simple-deprules.d/media | 20 +--- |
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config/simple-deprules.d/media-libs | 30 ++---- |
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config/simple-deprules.d/misc | 6 +- |
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config/simple-deprules.d/net | 21 +--- |
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config/simple-deprules.d/nvidia | 22 ++-- |
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config/simple-deprules.d/sci | 34 +++---- |
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config/simple-deprules.d/sci-libs | 35 ++----- |
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config/simple-deprules.d/selfdeps | 22 ---- |
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config/simple-deprules.d/selfdeps.d/sci-CRAN | 23 ++--- |
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config/simple-deprules.d/sys | 32 +++--- |
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config/simple-deprules.d/system.set | 39 ++----- |
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config/simple-deprules.d/unknown | 5 +- |
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config/simple-deprules.d/x11 | 12 +-- |
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roverlay/depres/simpledeprule/abstractrules.py | 10 +- |
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roverlay/depres/simpledeprule/rules.py | 6 +- |
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23 files changed, 195 insertions(+), 617 deletions(-) |
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|
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diff --git a/config/simple-deprules.d/R b/config/simple-deprules.d/R |
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index 9106deb..8edf111 100644 |
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--- a/config/simple-deprules.d/R |
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+++ b/config/simple-deprules.d/R |
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@@ -6,53 +6,43 @@ |
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#deptype all |
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|
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# using fuzzy dep matches |
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-~dev-lang/R :: R |
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+~dev-lang/R :: ^R$ |
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|
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dev-lang/R[tk] { |
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- tcl/tk 8.5 |
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- Tcl/Tk (>= 8.5) |
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- tcltk (but only for the GUI |
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-} |
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- |
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-# base packages that always assumed to be provided by dev-lang/R (taken from generate_ebuild) |
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-% { |
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- base |
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- compiler |
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- datasets |
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- graphics |
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- grDevices |
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- grid |
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- methods |
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- parallel |
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- splines |
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- stats |
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- stats4 |
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+ tcl/tk |
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tcltk |
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- tools |
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- utils |
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} |
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|
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-# FIXME, seems to be provided too |
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-% { |
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- stepfun |
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- ts |
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- package ts |
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- package ts (included in the R release) |
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-} |
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# modreg is in stats, according to https://stat.ethz.ch/pipermail/bioconductor/2010-June/034197.html |
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! :: modreg |
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|
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# R is always compiled with '--enabled-R-shlib' |
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! { |
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- R must be compiled with --enable-R-shlib if the server is to be built |
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- R must be compiled with --enable-R-shlib if theserver is to be built |
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- R must be compiled with --enable-R-shlibif the server is to be built |
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- Download regular shlib (420 KB) from externalsource ('xls.getshlib()' or manually) |
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- R built as a shared object |
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- R built as a shared object. |
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- R built as a shared or static (R >= 2.7.0) library |
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- R built as a shared orstatic library |
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+ --enable-R-shlib |
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+ xls.getshlib |
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+ R built as a shared |
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R-0.64 or later |
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- Regular shlib must be obtained from an externalsource (use 'xls.getshlib()' or dl manually). |
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- dl regular shlib with 'xls.getshlib()'or manually (~420 KB) |
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+} |
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+ |
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+# base packages that always assumed to be provided by dev-lang/R (taken from generate_ebuild) |
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+% { |
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+ ^base$ |
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+ ^compiler$ |
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+ ^datasets$ |
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+ ^graphics$ |
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+ ^grDevices$ |
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+ ^grid$ |
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+ ^methods$ |
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+ ^parallel$ |
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+ ^splines$ |
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+ ^stats4? |
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+ ^tools$ |
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+ ^utils$ |
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+} |
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+ |
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+# FIXME, seems to be provided too |
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+% { |
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+ ^stepfun$ |
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+ ^ts$ |
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+ package.*ts |
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} |
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|
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diff --git a/config/simple-deprules.d/app b/config/simple-deprules.d/app |
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index 99ba3c3..6c086c4 100644 |
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--- a/config/simple-deprules.d/app |
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+++ b/config/simple-deprules.d/app |
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@@ -3,10 +3,7 @@ |
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app-admin/ec2-api-tools :: ec2-api-tools |
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|
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# FIXME zip or unzip? |
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-app-arch/zip :: zip |
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+app-arch/zip :: ^zip$ |
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|
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# FIXME: this is not satisfiable, latest dieharder version in portage is 2.28.1 |
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-app-crypt/dieharder { |
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- DieHarder library (>= 2.8.1) fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php |
140 |
- DieHarder library (>= 3.31.1) fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php |
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-} |
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+app-crypt/dieharder :: DieHarder |
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\ No newline at end of file |
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|
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diff --git a/config/simple-deprules.d/app-text b/config/simple-deprules.d/app-text |
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index 6e4cdd4..810178c 100644 |
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--- a/config/simple-deprules.d/app-text |
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+++ b/config/simple-deprules.d/app-text |
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@@ -1,35 +1,16 @@ |
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#deptype sys |
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|
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-app-text/antiword { |
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- Antiword (http://www.winfield.demon.nl/) forreading MS Word files |
154 |
- antiword for reading MS Word files |
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- Antiword (<http://www.winfield.demon.nl/>) forreading MS Word files |
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-} |
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+app-text/antiword :: Antiword |
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|
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~app-text/ghostscript-gpl :: ghostscript |
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|
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app-text/poppler { |
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- pdfinfo andpdftotext for reading PDF |
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- pdfinfo and pdftotext from Poppler(http://poppler.freedesktop.org/) for reading PDF |
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- pdftotext from Poppler(http://poppler.freedesktop.org/) for reading PDF |
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-} |
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- |
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-# pdflatex? |
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-app-text/texlive { |
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- (PDF)LaTeX (http://www.latex-project.org/) withpdfpages package for studentGrowthPlot option in visualizeSGPto bind together student growth plots into school catalogs. |
170 |
- (PDF)LaTeX (http://www.latex-project.org/) with'pdfpages' package for studentGrowthPlot option in visualizeSGPto bind together student growth plots into school catalogs. |
171 |
- (PDF)LaTeX for saveLatex() |
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-} |
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- |
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-app-text/poppler { |
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+ poppler |
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pdfinfo |
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+ pdftotext |
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} |
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|
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+# pdflatex? |
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+app-text/texlive :: LaTeX |
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|
183 |
~app-text/pandoc :: pandoc |
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-app-text/pandoc { |
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- pandoc (>= 1.12.3) -http://johnmacfarlane.net/pandoc |
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- pandoc with https support |
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- Package vignettes based on R Markdown v2 requirePandoc (http://pandoc.org). The function rst2pdf() andvignettes based on reStructuredText require rst2pdf(https://github.com/rst2pdf/rst2pdf). |
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-} |
189 |
- |
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|
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diff --git a/config/simple-deprules.d/compound_deps b/config/simple-deprules.d/compound_deps |
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index 963ee0f..b0c0133 100644 |
193 |
--- a/config/simple-deprules.d/compound_deps |
194 |
+++ b/config/simple-deprules.d/compound_deps |
195 |
@@ -2,50 +2,45 @@ |
196 |
|
197 |
( media-libs/fontconfig media-fonts/corefonts ) { |
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fontconfig and msttcorefonts |
199 |
- fontconfig and msttcorefonts recommended) |
200 |
} |
201 |
|
202 |
( net-libs/liboauth net-misc/curl ) { |
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- liboauth (>= 0.9.4) liboauth.sourceforge.net andlibcurl http://curl.haxx.se |
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+ liboauth.*curl |
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} |
206 |
|
207 |
# FIXME |
208 |
( sci-libs/blas-atlas dev-util/nvidia-cuda-toolkit ) { |
209 |
- Atlas development build as well as a Nvidia GPU withCUDA support |
210 |
+ Atlas.*Nvidia GPU.*CUDA |
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} |
212 |
|
213 |
|| ( dev-libs/libxml2 dev-libs/expat ) { |
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- Daniel Veillard's libxml(ftp://ftp.gnome.org/pub/GNOME/sources/libxml/)and/orJim Clark's expat (http://www.jclark.com/xml) |
215 |
- Daniel Veillard's libxml(ftp://ftp.gnome.org/pub/GNOME/stable/sources/libxml/)and/orJim Clark's expat (http://www.jclark.com/xml) |
216 |
+ libxml.*expat |
217 |
} |
218 |
|
219 |
( media-libs/tiff >=sci-libs/fftw-3 ) { |
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- optional libtiff and fftw3 |
221 |
+ libtiff.*fftw3 |
222 |
} |
223 |
|
224 |
( sci-libs/gdal sci-libs/proj ) { |
225 |
- for building from source: GDAL >= 1.3.1 && GDAL < 1.6.0 (until tested) library and PROJ.4 (proj >= 4.4.9) |
226 |
- for building from source: GDAL >= 1.3.1 library and PROJ.4 (proj >= 4.4.9) |
227 |
- for building from source: GDAL >= 1.3.1 library and PROJ.4(proj >= 4.4.9) |
228 |
- for building from source: GDAL >= 1.6.0 library and PROJ.4(proj >= 4.4.9) |
229 |
+ GDAL.*PROJ.4 |
230 |
} |
231 |
|
232 |
( dev-libs/mpfr dev-libs/gmp ) { |
233 |
- http://mpfr.org/) and GMP (GNU Multiple Precision library |
234 |
+ mpfr.*GMP |
235 |
} |
236 |
|
237 |
|| ( media-gfx/imagemagick media-gfx/graphicsmagick ) { |
238 |
- ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) for saveGIF() |
239 |
+ ImageMagick.*GraphicsMagick |
240 |
} |
241 |
|
242 |
|| ( media-gfx/imagemagick media-gfx/graphicsmagick app-office/lyx ) { |
243 |
- ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) or LyX(http://www.lyx.org) for saveGIF() |
244 |
+ ImageMagick.*GraphicsMagick.*LyX |
245 |
} |
246 |
|
247 |
|| ( media-libs/tiff virtual/jpeg ) { |
248 |
- libtiff and/or libjpeg |
249 |
+ libtiff.*libjpeg |
250 |
} |
251 |
|
252 |
( virtual/blas virtual/lapack ) { |
253 |
- BLAS/LAPACK libraries |
254 |
+ BLAS.*LAPACK |
255 |
} |
256 |
|
257 |
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev |
258 |
index 89759fc..faa01d9 100644 |
259 |
--- a/config/simple-deprules.d/dev |
260 |
+++ b/config/simple-deprules.d/dev |
261 |
@@ -10,74 +10,34 @@ dev-cpp/gtkmm :: gtkmm-2.4 |
262 |
} |
263 |
|
264 |
# FIXME |
265 |
-dev-db/unixODBC { |
266 |
- An ODBC driver manager and drivers. See README. |
267 |
- An ODBC3 driver manager and drivers. |
268 |
- An ODBC3 driver manager and drivers. See README. |
269 |
- ODBC support and a back end database |
270 |
-} |
271 |
+dev-db/unixODBC :: ODBC |
272 |
|
273 |
-dev-java/ant :: ant |
274 |
+dev-java/ant :: ^ant$ |
275 |
dev-java/jdbc-postgresql :: PostgreSQL JDBCdriver |
276 |
|
277 |
- |
278 |
-# try to slot-match dev-lang/python, but use known slots only |
279 |
-~dev-lang/python:slotparts=2:restrict=2.7,3.2,3.3,3.4 { |
280 |
- python |
281 |
- python headers |
282 |
-} |
283 |
# else fall back to fuzzy |
284 |
~dev-lang/python { |
285 |
- python |
286 |
+ ^python |
287 |
} |
288 |
# lowest python version in portage: 2.7 (2.6 masked) |
289 |
dev-lang/python { |
290 |
- Python (>= 2.4) to run Asciidoc(http://www.python.org/) |
291 |
- Python 2.7.x or Python 3.2.x-3.4.x |
292 |
+ ^Python |
293 |
} |
294 |
|
295 |
- |
296 |
dev-lang/lua :: lua version>= 5.1.4 |
297 |
~dev-lang/lua :: lua |
298 |
|
299 |
-~dev-tex/pgf { |
300 |
- pgf |
301 |
-} |
302 |
+~dev-tex/pgf :: ^pgf$ |
303 |
|
304 |
->=dev-tex/pgf-2.10 { |
305 |
- pgf (>=2.10) (http://sourceforge.net/projects/pgf/)for the vignette |
306 |
-} |
307 |
+>=dev-tex/pgf-2.10 :: pgf.*>=2.10 |
308 |
|
309 |
-~dev-tcltk/bwidget { |
310 |
- bwidget |
311 |
- Tcl/Tk extensions BWidget |
312 |
-} |
313 |
+~dev-tcltk/bwidget :: bwidget |
314 |
|
315 |
~dev-tcltk/tktable :: tktable |
316 |
|
317 |
-dev-util/cmake { |
318 |
- cmake |
319 |
- cmake (http://www.cmake.org) |
320 |
-} |
321 |
- |
322 |
-~dev-python/numpy { |
323 |
- numpy |
324 |
-} |
325 |
+dev-util/cmake :: cmake |
326 |
|
327 |
-# FIXME: the jdk rules are not quite correct, |
328 |
-# virtual/jdk:1.7 (probably) works for some packages, too |
329 |
-# |
330 |
-~virtual/jdk:slotparts=i1.6:restrict=1.6,6.0 { |
331 |
- java |
332 |
- Java version |
333 |
- java runtime |
334 |
-} |
335 |
- |
336 |
-~virtual/jdk:slotparts=i1.7:restrict=1.7,7.0 { |
337 |
- java |
338 |
- Java version |
339 |
- java runtime |
340 |
-} |
341 |
+~dev-python/numpy :: numpy |
342 |
|
343 |
# slot-relative rules take precedence |
344 |
# TODO: slot-restricted rules should get a lower priority |
345 |
|
346 |
diff --git a/config/simple-deprules.d/dev-libs b/config/simple-deprules.d/dev-libs |
347 |
index b46d2a6..b0faa08 100644 |
348 |
--- a/config/simple-deprules.d/dev-libs |
349 |
+++ b/config/simple-deprules.d/dev-libs |
350 |
@@ -1,95 +1,52 @@ |
351 |
#deptype sys |
352 |
|
353 |
-~dev-libs/atk :: ATK |
354 |
+~dev-libs/atk :: ^ATK$ |
355 |
|
356 |
~dev-libs/openssl :: OpenSSL |
357 |
|
358 |
-~dev-libs/boost { |
359 |
- boost library |
360 |
- boost |
361 |
-} |
362 |
-dev-libs/boost { |
363 |
- Boost C++ libraries (1.31 or greater) |
364 |
- Boost library (>= 1.34.0) from http://www.boost.org |
365 |
- Boost library (>= 1.34.0) fromhttp://www.boost.org |
366 |
- Boost library from http://www.boost.org |
367 |
- Boost libraryfrom http://www.boost.org |
368 |
- boost headers for smart pointers |
369 |
- The Boost 'program_options' library(http://boost.org) is required. |
370 |
- Boost (or the BoostHeaders package) |
371 |
-} |
372 |
+~dev-libs/boost :: boost |
373 |
|
374 |
-~dev-libs/glib { |
375 |
- glib |
376 |
- glib2 |
377 |
-} |
378 |
+~dev-libs/glib :: glib |
379 |
|
380 |
~dev-libs/gmp { |
381 |
libgmp |
382 |
- gmp |
383 |
-} |
384 |
-~dev-libs/gmp { |
385 |
- GMP (GNU MP bignum library |
386 |
- GMP (GNU MP bignum library) |
387 |
- GMP (GNU Multiple Precision library |
388 |
- http://gmplib.org/) |
389 |
+ ^gmp |
390 |
+ gmplib |
391 |
} |
392 |
|
393 |
~dev-libs/libffi :: libffi |
394 |
|
395 |
~dev-libs/libpcre { |
396 |
- libpcre |
397 |
pcre |
398 |
} |
399 |
|
400 |
~dev-libs/libxml2 { |
401 |
- xml |
402 |
- xml2 |
403 |
- libxml |
404 |
- libxml2 |
405 |
+ ^xml |
406 |
+ ^libxml |
407 |
} |
408 |
|
409 |
~dev-libs/libxslt :: libxslt |
410 |
|
411 |
dev-libs/mpc { |
412 |
- and MPC (Multiple Precision ComplexLibrary |
413 |
- http://www.multiprecision.org/) |
414 |
+ ^mpc$ |
415 |
+ multi.*precision |
416 |
} |
417 |
|
418 |
-~dev-libs/mpfr { |
419 |
- MPFR (MP Floating-Point Reliable Library |
420 |
- mpfr |
421 |
- http://mpfr.org/) |
422 |
-} |
423 |
+~dev-libs/mpfr :: mpfr |
424 |
+ |
425 |
# FIXME versions -> fuzzy |
426 |
-dev-libs/quantlib { |
427 |
- QuantLib libraries must be installed |
428 |
- QuantLib library (>= 0.8.1) from http://quantlib.org |
429 |
- QuantLib library (>= 0.9.0) from http://quantlib.org |
430 |
- QuantLib library (>= 0.9.7) from http://quantlib.org |
431 |
- QuantLib library (>= 0.9.7) fromhttp://quantlib.org |
432 |
- QuantLib library (>= 0.9.9) fromhttp://quantlib.org |
433 |
- QuantLib library from http://quantlib.org |
434 |
-} |
435 |
+dev-libs/quantlib :: QuantLib |
436 |
|
437 |
~dev-libs/quantlib { |
438 |
QuantLib library |
439 |
} |
440 |
|
441 |
-~dev-libs/xerces-c { |
442 |
- xerces-c |
443 |
- libxerces-c |
444 |
-} |
445 |
+~dev-libs/xerces-c :: xerces-c |
446 |
|
447 |
~sys-devel/clang { |
448 |
clang |
449 |
} |
450 |
|
451 |
-dev-libs/geoip { |
452 |
- GeoIP from MaxMinds |
453 |
-} |
454 |
+dev-libs/geoip :: GeoIP |
455 |
|
456 |
-dev-libs/icu { |
457 |
- ICU4C (>= 50 |
458 |
- ICU4C (>= 52 |
459 |
-} |
460 |
+dev-libs/icu :: ICU4C |
461 |
|
462 |
diff --git a/config/simple-deprules.d/dot_remap b/config/simple-deprules.d/dot_remap |
463 |
deleted file mode 100644 |
464 |
index 03aa2f4..0000000 |
465 |
--- a/config/simple-deprules.d/dot_remap |
466 |
+++ /dev/null |
467 |
@@ -1,134 +0,0 @@ |
468 |
-#! NOPARSE |
469 |
-# |
470 |
-# !!! This file should no longer be necessary |
471 |
-# (the dynamic selfdep pool is able to remap dots automatically) |
472 |
-# |
473 |
- |
474 |
-#deptype pkg,selfdep |
475 |
- |
476 |
-~sci-R/aroma_affymetrix :: aroma.affymetrix |
477 |
-~sci-R/aroma_apd :: aroma.apd |
478 |
-~sci-R/aroma_core :: aroma.core |
479 |
-~sci-R/aroma_light :: aroma.light |
480 |
- |
481 |
-~sci-R/bio_infer :: bio.infer |
482 |
- |
483 |
-~sci-R/Ckmeans_1d_dp :: Ckmeans.1d.dp |
484 |
-~sci-R/clim_pact :: clim.pact |
485 |
-~sci-R/compute_es :: compute.es |
486 |
-~sci-R/conf_design :: conf.design |
487 |
- |
488 |
-~sci-R/data_table :: data.table |
489 |
-~sci-R/DoE_base :: DoE.base |
490 |
-~sci-R/DoE_wrapper :: DoE.wrapper |
491 |
- |
492 |
-~sci-R/ergm_userterms :: ergm.userterms |
493 |
- |
494 |
-~sci-R/FrF2_catlg128 :: FrF2.catlg128 |
495 |
-~sci-R/FunciSNP :: FunciSNP.data |
496 |
-~sci-R/futile_any :: futile.any |
497 |
-~sci-R/futile_logger :: futile.logger |
498 |
-~sci-R/futile_matrix :: futile.matrix |
499 |
-~sci-R/futile_options :: futile.options |
500 |
-~sci-R/futile_paradigm :: futile.paradigm |
501 |
- |
502 |
-~sci-R/gamlss_data :: gamlss.data |
503 |
-~sci-R/gamlss_dist :: gamlss.dist |
504 |
-~sci-R/gamlss_nl :: gamlss.nl |
505 |
-~sci-R/gamlss_tr :: gamlss.tr |
506 |
-~sci-R/gamlss_util :: gamlss.util |
507 |
-~sci-R/GO_db :: GO.db |
508 |
- |
509 |
-~sci-R/haplo_score :: haplo_score |
510 |
-~sci-R/haplo_stats :: haplo_stats |
511 |
-~sci-R/heapmap_plus :: heatmap.plus |
512 |
- |
513 |
-~sci-R/lava_tobit :: lava.tobit |
514 |
- |
515 |
-~sci-R/minpack_lm :: minpack.lm |
516 |
- |
517 |
-~sci-R/opencpu_encode :: opencpu.encode |
518 |
-~sci-R/openNLPmodels_en :: openNLPmodels.en |
519 |
-~sci-R/openNLPmodels_es :: openNLPmodels.es |
520 |
-~sci-R/operator_tools :: operator.tools |
521 |
-~sci-R/orloca_es :: orloca.es |
522 |
-~sci-R/oro_dicom :: oro.dicom |
523 |
-~sci-R/oro_nifti :: oro.nifti |
524 |
- |
525 |
-~sci-R/org_Ag_eg_db :: org.Ag.eg.db |
526 |
-~sci-R/org_At_tair_db :: org.At.tair.db |
527 |
-~sci-R/org_Bt_eg_db :: org.Bt.eg.db |
528 |
-~sci-R/org_Ce_eg_db :: org.Ce.eg.db |
529 |
-~sci-R/org_Cf_eg_db :: org.Cf.eg.db |
530 |
-~sci-R/org_Dm_eg_db :: org.Dm.eg.db |
531 |
-~sci-R/org_Dr_eg_db :: org.Dr.eg.db |
532 |
-~sci-R/org_EcK12_eg_db :: org.EcK12.eg.db |
533 |
-~sci-R/org_EcSakai_eg_db :: org.EcSakai.eg.db |
534 |
-~sci-R/org_Gg_eg_db :: org.Gg.eg.db |
535 |
-~sci-R/org_Hs_eg_db :: org.Hs.eg.db |
536 |
-~sci-R/org_Mm_eg_db :: org.Mm.eg.db |
537 |
-~sci-R/org_Mmu_eg_db :: org.Mmu.eg.db |
538 |
-~sci-R/org_Pf_plasmo_db :: org.Pf.plasmo.db |
539 |
-~sci-R/org_Pt_eg_db :: org.Pt.eg.db |
540 |
-~sci-R/org_Rn_eg_db :: org.Rn.eg.db |
541 |
-~sci-R/org_Sc_sgd_db :: org.Sc.sgd.db |
542 |
-~sci-R/org_Sco_eg_db :: org.Sco.eg.db |
543 |
-~sci-R/org_Ss_eg_db :: org.Ss.eg.db |
544 |
-~sci-R/org_Xl_eg_db :: org.Xl.eg.db |
545 |
- |
546 |
-~sci-R/R_cache :: R.cache |
547 |
-~sci-R/RcmdrPlugin_IPSUR :: RcmdrPlugin.IPSUR |
548 |
-~sci-R/R_devices :: R.devices |
549 |
-~sci-R/R_filesets :: R.filesets |
550 |
-~sci-R/R_huge :: R.huge |
551 |
-~sci-R/R_matlab :: R.matlab |
552 |
-~sci-R/R_methodsS3 :: R.methodsS3 |
553 |
-~sci-R/ROI_plugin_glpk :: ROI.plugin.glpk |
554 |
-~sci-R/ROI_plugin_quadprog :: ROI.plugin.quadprog |
555 |
-~sci-R/ROI_plugin_symphony :: ROI.plugin.symphony |
556 |
-~sci-R/R_oo :: R.oo |
557 |
-~sci-R/rpart_plot :: rpart.plot |
558 |
-~sci-R/R_rsp :: R.rsp |
559 |
-~sci-R/RSQLite_extfuns :: RSQLite.extfuns |
560 |
-~sci-R/R_utils :: R.utils |
561 |
- |
562 |
-~sci-R/Sim_DiffProc :: Sim.DiffProc |
563 |
-~sci-R/SNPMaP_cdm :: SNPMaP.cdm |
564 |
-~sci-R/survJamda_data :: survJamda.data |
565 |
- |
566 |
-~sci-R/tawny_types :: tawny.types |
567 |
- |
568 |
-~sci-R/DO_db :: DO.db |
569 |
-~sci-R/IlluminaHumanMethylation27k_db :: IlluminaHumanMethylation27k.db |
570 |
-~sci-R/IlluminaHumanMethylation450k_db :: IlluminaHumanMethylation450k.db |
571 |
-~sci-R/KEGG_db :: KEGG.db |
572 |
-~sci-R/SNPlocs_Hsapiens_dbSNP_20090506 :: SNPlocs.Hsapiens.dbSNP.20090506 |
573 |
-~sci-R/SNPlocs_Hsapiens_dbSNP_20100427 :: SNPlocs.Hsapiens.dbSNP.20100427 |
574 |
-~sci-R/SNPlocs_Hsapiens_dbSNP_20101109 :: SNPlocs.Hsapiens.dbSNP.20101109 |
575 |
-~sci-R/gahgu133plus2_db :: gahgu133plus2.db |
576 |
-~sci-R/hgfocus_db :: hgfocus.db |
577 |
-~sci-R/hgu133a_db :: hgu133a.db |
578 |
-~sci-R/hgu133plus2_db :: hgu133plus2.db |
579 |
-~sci-R/hgu95a_db :: hgu95a.db |
580 |
-~sci-R/hgu95av2_db :: hgu95av2.db |
581 |
-~sci-R/hgug4112a_db :: hgug4112a.db |
582 |
-~sci-R/hu6800_db :: hu6800.db |
583 |
-~sci-R/illuminaHumanv1_db :: illuminaHumanv1.db |
584 |
-~sci-R/nutshell_bbdb :: nutshell.bbdb |
585 |
-~sci-R/reactome_db :: reactome.db |
586 |
- |
587 |
-~sci-R/RmiR_Hs_miRNA :: RmiR.Hs.miRNA |
588 |
-~sci-R/TxDb_Hsapiens_UCSC_hg18_knownGene :: TxDb.Hsapiens.UCSC.hg18.knownGene |
589 |
-~sci-R/TxDb_Hsapiens_UCSC_hg19_knownGene :: TxDb.Hsapiens.UCSC.hg19.knownGene |
590 |
-~sci-R/bigmemory_sri :: bigmemory.sri |
591 |
-~sci-R/gamlss_add :: gamlss.add |
592 |
-~sci-R/gemtc_jar :: gemtc.jar |
593 |
-~sci-R/haplo_stats :: haplo.stats |
594 |
-~sci-R/nutshell_audioscrobbler :: nutshell.audioscrobbler |
595 |
-~sci-R/pd_charm_hg18_example :: pd.charm.hg18.example |
596 |
-~sci-R/pd_mapping250k_nsp :: pd.mapping250k.nsp |
597 |
-~sci-R/pd_mapping250k_sty :: pd.mapping250k.sty |
598 |
-~sci-R/pd_mapping50k_hind240 :: pd.mapping50k.hind240 |
599 |
-~sci-R/pd_mapping50k_xba240 :: pd.mapping50k.xba240 |
600 |
-~sci-R/simdat_base :: simdat.base |
601 |
- |
602 |
|
603 |
diff --git a/config/simple-deprules.d/ignored_text b/config/simple-deprules.d/ignored_text |
604 |
index 097f004..b05353d 100644 |
605 |
--- a/config/simple-deprules.d/ignored_text |
606 |
+++ b/config/simple-deprules.d/ignored_text |
607 |
@@ -2,78 +2,53 @@ |
608 |
|
609 |
# ignored text |
610 |
! { |
611 |
- available at <http://csound.sourceforge.net/>. See<http://playitbyr.org/csound.html> for more guidance on settingup Csound. |
612 |
- available at<http://csound.sourceforge.net/>. This package uses the sharedlibrary file |
613 |
- becauseBRugs does not support other platforms/OS right now. |
614 |
- binary Linux distributions often package thelibrary separately from the executible file |
615 |
- it is an extension for the R package tcltk that consists of Tclscripts. See README file. |
616 |
- all other functions are stand alone) |
617 |
- see also the topic 'SoPhy' in the documentation |
618 |
- see also the topic'SoPhy' in the documentation |
619 |
- see file README |
620 |
- see README |
621 |
- see README. |
622 |
- see ./README. |
623 |
- see the cloudRmpi manual (vignette)for details. |
624 |
+ does not support |
625 |
+ all other functions are stand alone |
626 |
+ documentation |
627 |
+ README |
628 |
+ INSTALL |
629 |
+ so for instance |
630 |
+ optional |
631 |
+ suggested |
632 |
+ See the |
633 |
see topic SoPhy below |
634 |
- so for instance onDebian and Ubuntu you would need the "libcsound64-dev" package.See the package web site for more guidance on setup andconfiguration. |
635 |
- so for instance onDebian and Ubuntu you would need the "libcsound64-dev" package.See the web site below for more guidance on setup. |
636 |
some Windows variants are supported experimentally |
637 |
- your mileage may vary) |
638 |
- optional) |
639 |
- heavily suggested) |
640 |
- and Windows |
641 |
- hence Windows or Linux |
642 |
- $distributions package thelibrary file separately from the executible |
643 |
- libraries(See the INSTALL file) |
644 |
- or INSTALL.windows under Windows |
645 |
- standard unix tools (e.g. |
646 |
- rgdal OSX binary packages are also available at the samesite. |
647 |
- rgdal OSX binary packages are also available at the same site. |
648 |
- probably) |
649 |
- Linux and Mac |
650 |
- MPICH2 (>= 1.4.1p1) on Windows |
651 |
+ your mileage may vary |
652 |
+ Windows |
653 |
+ distributions package |
654 |
+ distributions often package |
655 |
+ probably |
656 |
which is included with standard Mac and Windowsinstallations of Csound. Some Linux distributions package thelibrary file separately from the executible |
657 |
- playitbyr creates sound using the csound package |
658 |
- which requires the free and open source software synthesizerCsound |
659 |
- A valid copy of the Csound library must present.Csound can be downloaded Thelibrary is included in the Windows and Mac OS X binaries |
660 |
- A valid copy of the Csound library must present.Csound can be downloaded Thelibrary is included in the Windows |
661 |
binary Linux distributions often package the library separatelyfrom the executible file |
662 |
- so for instance on Debian and Ubuntuyou would need the "libcsound64-dev" package. |
663 |
For the MERLIN wrapper |
664 |
+ Debian |
665 |
+ Ubuntu |
666 |
Mac |
667 |
- Mac OSX |
668 |
- Mac OS X |
669 |
- Mac OS X binaries |
670 |
- Mac.Parallel HDF5 |
671 |
+ OSX |
672 |
+ OS X |
673 |
Linux/64bit |
674 |
sources are included for other OSes. |
675 |
see readme.txt |
676 |
- so for instance on Debian |
677 |
- so for instance onDebian |
678 |
- Ubuntu you would need the "libcsound64-dev" package.See the package web site for more guidance on setup andconfiguration. |
679 |
- Ubuntuyou would need the "libcsound64-dev" package. |
680 |
- which is included with standard Mac |
681 |
+ so for instance |
682 |
+ you would need the |
683 |
which requires the free |
684 |
- drivers. |
685 |
+ drivers |
686 |
License |
687 |
its development files |
688 |
- library (version2.2.0 or later) |
689 |
- libraries(See README.REQ) |
690 |
- Google Chrome for Windows |
691 |
+ ^library |
692 |
+ Google Chrome |
693 |
for externalization |
694 |
writing some graphicformats |
695 |
- available athttp://www.monetdb.org |
696 |
- it is used in the demos too). |
697 |
+ available at |
698 |
+ it is used in the demos too |
699 |
headers |
700 |
- OpenCSW. |
701 |
+ OpenCSW |
702 |
+ Linux |
703 |
+ precision AMD or Nvidia GPU |
704 |
+ ^and$ |
705 |
+ in addition |
706 |
} |
707 |
|
708 |
-# that's a hardware requirement |
709 |
-! :: double-precision AMD or Nvidia GPU |
710 |
- |
711 |
-% :: Linux |
712 |
- |
713 |
# ignore "Windows" in dependency fields: |
714 |
# (a) there's OS_Type for OS restrictions |
715 |
# (b) it's a filler word sometimes ("xyz on Solaris, Linux and Windows") |
716 |
@@ -89,28 +64,12 @@ |
717 |
! :: None |
718 |
|
719 |
! { |
720 |
- Will use djmrgl or rgl packages for rendering ifpresent |
721 |
- Will use djmrgl or rgl packages for rendering if present |
722 |
- SYMPHONY for Windows (sources included for otherOSes) |
723 |
+ Will use djmrgl or rgl packages for rendering |
724 |
SYMPHONY libraries |
725 |
} |
726 |
|
727 |
-# ignore OSX recommendations |
728 |
-! { |
729 |
- GDAL OSX frameworks built by William Kyngesburye at http://www.kyngchaos.com/ may be used for source installs on OSX |
730 |
- GDAL OSXframeworks built by William Kyngesburye athttp://www.kyngchaos.com/ may be used for source installs onOSX |
731 |
- GDAL OSXframeworks built by William Kyngesburye athttp://www.kyngchaos.com/ may be used for source installs onOSX. |
732 |
-} |
733 |
- |
734 |
-! { |
735 |
- GEOS OSX frameworks built byWilliam Kyngesburye at http://www.kyngchaos.com/ may be usedfor source installs on OSX. |
736 |
-} |
737 |
- |
738 |
# SoPhy splits its Depends field into windows and linux |
739 |
! { |
740 |
- windows:Tiff for windows |
741 |
- windows: Tiff (libtiff3.dll) |
742 |
- windows: Tiff(libtiff3.dll) |
743 |
zlib1.dll and jpeg62.dll |
744 |
} |
745 |
|
746 |
|
747 |
diff --git a/config/simple-deprules.d/media b/config/simple-deprules.d/media |
748 |
index 41d8a03..3392d87 100644 |
749 |
--- a/config/simple-deprules.d/media |
750 |
+++ b/config/simple-deprules.d/media |
751 |
@@ -12,7 +12,7 @@ media-sound/csound { |
752 |
|
753 |
#deptype all |
754 |
media-gfx/imagemagick { |
755 |
- Image Magick (for reading non PPM format) |
756 |
+ Image Magick |
757 |
} |
758 |
#deptype sys |
759 |
|
760 |
@@ -23,25 +23,15 @@ media-gfx/graphviz :: dot from graphviz |
761 |
} |
762 |
|
763 |
media-gfx/swftools { |
764 |
- SWF Tools (http://swftools.org) forsaveSWF() |
765 |
- SWF Tools (http://swftools.org) for saveSWF() |
766 |
+ SWF.*Tools |
767 |
} |
768 |
|
769 |
virtual/ffmpeg { |
770 |
- FFmpeg (http://ffmpeg.org) for saveVideo() |
771 |
- FFmpeg(http://ffmpeg.org) for saveVideo() |
772 |
ffmpeg |
773 |
} |
774 |
|
775 |
-media-gfx/dcraw { |
776 |
- dcraw(for reading RAW images). |
777 |
- dcraw (for readingRAW images). |
778 |
-} |
779 |
+media-gfx/dcraw :: dcraw |
780 |
|
781 |
-media-libs/fontconfig { |
782 |
- fontconfig |
783 |
-} |
784 |
+media-libs/fontconfig :: fontconfig |
785 |
|
786 |
-media-fonts/corefonts { |
787 |
- msttcorefonts |
788 |
-} |
789 |
+media-fonts/corefonts :: msttcorefonts |
790 |
|
791 |
diff --git a/config/simple-deprules.d/media-libs b/config/simple-deprules.d/media-libs |
792 |
index 8b7ba10..799335f 100644 |
793 |
--- a/config/simple-deprules.d/media-libs |
794 |
+++ b/config/simple-deprules.d/media-libs |
795 |
@@ -3,23 +3,15 @@ |
796 |
~media-libs/flac :: flac |
797 |
|
798 |
# FIXME: some packages write optional deps into SystemRequirements (e.g. rgl from CRAN) |
799 |
-media-libs/freetype :: FreeType (optional) |
800 |
~media-libs/freetype :: freetype |
801 |
media-libs/freetype:2 :: recommended: freetype2 |
802 |
|
803 |
-media-libs/gd { |
804 |
- libgd (>= 2.0.28 http://www.boutell.com/gd/) |
805 |
- libgd (>= 2.0.29 http://www.boutell.com/gd/) |
806 |
- libgd (freetype2 |
807 |
-} |
808 |
+media-libs/gd :: libgd |
809 |
+ |
810 |
+media-libs/libpng :: libpng |
811 |
|
812 |
-media-libs/libpng { |
813 |
- libpng(>=1.2.9 |
814 |
- libpng (optional) |
815 |
- libpng(optional) |
816 |
-} |
817 |
~media-libs/libpng { |
818 |
- png |
819 |
+ png$ |
820 |
libpng |
821 |
} |
822 |
|
823 |
@@ -27,13 +19,9 @@ media-libs/libpng { |
824 |
|
825 |
~media-libs/netpbm :: netpbm |
826 |
|
827 |
-media-libs/raptor :: libraptor2 (>= 2.0.0 http://librdf.org/raptor/) |
828 |
+media-libs/raptor :: libraptor |
829 |
|
830 |
-media-libs/tiff { |
831 |
- linux: libtiff (and libtiff-devel) |
832 |
- optional libtiff |
833 |
- optionally libtiff |
834 |
-} |
835 |
+media-libs/tiff :: libtiff |
836 |
|
837 |
~media-libs/tiff { |
838 |
tiff |
839 |
@@ -41,8 +29,4 @@ media-libs/tiff { |
840 |
libtiff-devel |
841 |
} |
842 |
|
843 |
-virtual/jpeg { |
844 |
- libjpeg |
845 |
- jpeg |
846 |
- jpeg libraries |
847 |
-} |
848 |
+virtual/jpeg :: jpeg |
849 |
|
850 |
diff --git a/config/simple-deprules.d/misc b/config/simple-deprules.d/misc |
851 |
index 9157f64..f403705 100644 |
852 |
--- a/config/simple-deprules.d/misc |
853 |
+++ b/config/simple-deprules.d/misc |
854 |
@@ -1,9 +1,7 @@ |
855 |
-dev-vcs/git { |
856 |
- git |
857 |
-} |
858 |
+dev-vcs/git :: ^git$ |
859 |
|
860 |
>=app-emulation/wine-1.5.26 { |
861 |
- wine (>= wine-1.5.26) |
862 |
+ wine.*1.5.26 |
863 |
} |
864 |
|
865 |
|
866 |
|
867 |
diff --git a/config/simple-deprules.d/net b/config/simple-deprules.d/net |
868 |
index ab87ea8..a2e6184 100644 |
869 |
--- a/config/simple-deprules.d/net |
870 |
+++ b/config/simple-deprules.d/net |
871 |
@@ -1,31 +1,20 @@ |
872 |
#deptype sys |
873 |
|
874 |
-net-misc/curl { |
875 |
- curl (version 7.12.0) http://curl.haxx.se |
876 |
- curl (version 7.12.0 or higher)<http://curl.haxx.se> |
877 |
- curl (version 7.12.0 or higher) http://curl.haxx.se |
878 |
- curl (version 7.12.0 or higher) <http://curl.haxx.se> |
879 |
- curl (version 7.14.0 or higher) http://curl.haxx.se |
880 |
- you will often have toexplicitly install libcurl-devel to have the header files andthe libcurl library. |
881 |
- libcurl (version 7.14.0 or higher)http://curl.haxx.se. On Linux systems |
882 |
- you will oftenhave to explicitly install libcurl-devel to have theheader files |
883 |
- libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb). |
884 |
-} |
885 |
+net-misc/curl :: curl |
886 |
~net-misc/curl { |
887 |
curl |
888 |
libcurl |
889 |
- the libcurl library. |
890 |
+ the libcurl library |
891 |
} |
892 |
|
893 |
# FIXME |
894 |
net-libs/czmq :: libzmq |
895 |
|
896 |
-net-libs/zeromq { |
897 |
- or ZeroMQ library >=4.0.4. Solaris 10 needs ZeroMQ library 4.0.7 |
898 |
-} |
899 |
+net-libs/zeromq :: ZeroMQ |
900 |
|
901 |
net-misc/s3cmd :: s3cmd |
902 |
|
903 |
virtual/ssh { |
904 |
- ssh daemon on the server side only:see the rreval manual (vignette) for details. |
905 |
+ ^ssh |
906 |
+ ssh$ |
907 |
} |
908 |
|
909 |
diff --git a/config/simple-deprules.d/nvidia b/config/simple-deprules.d/nvidia |
910 |
index ed77098..69a5775 100644 |
911 |
--- a/config/simple-deprules.d/nvidia |
912 |
+++ b/config/simple-deprules.d/nvidia |
913 |
@@ -2,34 +2,24 @@ |
914 |
|
915 |
# lowest cuda version in portage is 4.2.9 |
916 |
dev-util/nvidia-cuda-toolkit { |
917 |
- NVIDIA CUDA Toolkit (>= release 3.0) |
918 |
- Nvidia CUDAToolkit (>= release 3.0) |
919 |
- Nvidia's CUDA toolkit (>= release 2.3) |
920 |
- NVIDIA CUDA Toolkit 3.1 or above |
921 |
- NVIDIA CUDAtoolkit |
922 |
- NVIDIA CUDA Toolkit (>= release 4.0) |
923 |
+ NVIDIA.*CUDA.*Toolkit |
924 |
} |
925 |
|
926 |
>=dev-util/nvidia-cuda-toolkit-5.0 { |
927 |
- Nvidia's CUDA toolkit (>= release 5.0) |
928 |
+ Nvidia's CUDA toolkit.*5.0 |
929 |
} |
930 |
|
931 |
# FIXME cuda-toolkit or sdk? |
932 |
dev-util/nvidia-cuda-toolkit { |
933 |
- nvcc (>= release 2.1) |
934 |
- nvcc (>= release 2.1) nVidia GPU (compute number >=1.3) |
935 |
- nvcc (release 2.3) NVIDIA Cuda Compiler driver |
936 |
- nvcc (release 3.0) NVIDIA Cuda Compiler driver |
937 |
- nvcc (release >= 3.1) (NVIDIA Cuda Compilerdriver) |
938 |
- nvcc release 3.1 (NVIDIA Cuda Compiler driver) |
939 |
+ nvcc |
940 |
} |
941 |
|
942 |
>=dev-util/nvidia-cuda-toolkit-4.1 { |
943 |
- Nvidia's CUDA toolkit (release >= 4.1) |
944 |
+ Nvidia's CUDA toolkit.*4.1 |
945 |
} |
946 |
|
947 |
>=dev-util/nvidia-cuda-toolkit-4.5 { |
948 |
- Nvidia's CUDA toolkit (>= release 4.5) |
949 |
+ Nvidia's CUDA toolkit.*4.5 |
950 |
} |
951 |
|
952 |
~dev-util/nvidia-cuda-toolkit { |
953 |
@@ -37,5 +27,5 @@ dev-util/nvidia-cuda-toolkit { |
954 |
} |
955 |
|
956 |
>=x11-drivers/nvidia-drivers-270 { |
957 |
- Nvidia CUDA driver (>= 270.xx.xx) |
958 |
+ Nvidia CUDA driver.*270 |
959 |
} |
960 |
|
961 |
diff --git a/config/simple-deprules.d/sci b/config/simple-deprules.d/sci |
962 |
index 70521d9..6a93b72 100644 |
963 |
--- a/config/simple-deprules.d/sci |
964 |
+++ b/config/simple-deprules.d/sci |
965 |
@@ -2,8 +2,7 @@ |
966 |
|
967 |
# == geo == |
968 |
~sci-geosciences/gmt { |
969 |
- libgmt |
970 |
- gmt |
971 |
+ gmt$ |
972 |
} |
973 |
~sci-geosciences/grass :: grass |
974 |
|
975 |
@@ -11,44 +10,35 @@ |
976 |
|
977 |
~sci-mathematics/glpk { |
978 |
glpk |
979 |
- GLPK library package (e.g. |
980 |
} |
981 |
|
982 |
~sci-mathematics/jags :: jags |
983 |
-sci-mathematics/jags :: jags (see http://mcmc-jags.sourceforge.net) |
984 |
- |
985 |
-sci-mathematics/jags { |
986 |
- JAGS (>= 3.2.0) (or WinBUGS (>= 1.4) or OpenBUGS(>= 3.2.2)) |
987 |
-} |
988 |
|
989 |
# lowest octave version in portage is 3.4 |
990 |
sci-mathematics/octave { |
991 |
- Octave (>= 3.2.4) and its development files |
992 |
+ Octave |
993 |
} |
994 |
|
995 |
# lowest version in portage is 2.3.4-r1 |
996 |
sci-mathematics/pari { |
997 |
- PARI/GP >= 2.3.0 [strongly recommended for logkda()] |
998 |
- PARI/GP >= 2.3.0 [strongly recommended forlogkda()] |
999 |
pari/gp |
1000 |
} |
1001 |
|
1002 |
sci-mathematics/singular { |
1003 |
- Singular (http://www.singular.uni-kl.de) for exactcalculation of the MFR for graphs without splitting edges (onlyfor Unix systems). |
1004 |
+ Singular |
1005 |
} |
1006 |
|
1007 |
~sci-mathematics/yacas :: yacas |
1008 |
sci-mathematics/yacas { |
1009 |
- yacas (= 1.0.63) # instructions on home page |
1010 |
- yacas (>= 1.0.63) # instructions on home page |
1011 |
+ yacas |
1012 |
} |
1013 |
|
1014 |
sci-mathematics/octave { |
1015 |
- Octave (>= 3.2.4) |
1016 |
+ Octave |
1017 |
} |
1018 |
|
1019 |
sci-libs/netcdf { |
1020 |
- NetCDF4 (4.1 or later) libraries. |
1021 |
+ NetCDF4 |
1022 |
} |
1023 |
|
1024 |
# there's also sci-biology/clustalw-mpi |
1025 |
@@ -58,8 +48,8 @@ sci-biology/clustalw { |
1026 |
} |
1027 |
|
1028 |
sci-biology/ncbi-tools++ { |
1029 |
- ncbi-blast+ |
1030 |
- ncbi-tools++ |
1031 |
+ ncbi-blast\+ |
1032 |
+ ncbi-tools\+\+ |
1033 |
} |
1034 |
|
1035 |
sci-biology/kalign { |
1036 |
@@ -67,13 +57,13 @@ sci-biology/kalign { |
1037 |
} |
1038 |
|
1039 |
sci-mathematics/glpk { |
1040 |
- libglpk-dev onDebian/Ubuntu) |
1041 |
+ libglpk-dev |
1042 |
} |
1043 |
|
1044 |
#deptype all |
1045 |
|
1046 |
# some packages have glpk in "pkg" deps |
1047 |
-# (FIXME: does glpk in that context refer to an R package?) |
1048 |
+# FIXME: does glpk in that context refer to an R package? |
1049 |
~sci-mathematics/glpk { |
1050 |
glpk |
1051 |
} |
1052 |
@@ -94,14 +84,14 @@ sci-mathematics/rstudio { |
1053 |
|
1054 |
# lowest sci-physics/root version in portage is 5.32.03 |
1055 |
sci-physics/root { |
1056 |
- root_v5.32.01 <http://root.cern.ch> - See READMEfile for installation instructions. |
1057 |
+ root_v5.32.01 |
1058 |
} |
1059 |
|
1060 |
# == visualization == |
1061 |
|
1062 |
~sci-visualization/ggobi :: ggobi |
1063 |
|
1064 |
-sci-biology/merlin :: MERLIN(www.sph.umich.edu/csg/abecasis/merlin) must be installed andpointed to in the PATH environment variable. |
1065 |
+sci-biology/merlin :: MERLIN |
1066 |
|
1067 |
sci-visualization/gnuplot { |
1068 |
gnuplot |
1069 |
|
1070 |
diff --git a/config/simple-deprules.d/sci-libs b/config/simple-deprules.d/sci-libs |
1071 |
index 14da6a3..45506a8 100644 |
1072 |
--- a/config/simple-deprules.d/sci-libs |
1073 |
+++ b/config/simple-deprules.d/sci-libs |
1074 |
@@ -8,15 +8,13 @@ |
1075 |
# Use slot when the resolver can deal with them properly |
1076 |
>=sci-libs/fftw-3 { |
1077 |
fftw3 |
1078 |
- fftw3 (optional) |
1079 |
} |
1080 |
~sci-libs/fftw :: fftw |
1081 |
# Use slot when the resolver can deal with them properly |
1082 |
~sci-libs/fftw :: fftw3 |
1083 |
|
1084 |
sci-libs/gdal { |
1085 |
- GDAL library from http://www.gdal.org/download.html |
1086 |
- GDAL library from http://www.remotesensing.org/gdal/download.html |
1087 |
+ GDAL library |
1088 |
|
1089 |
} |
1090 |
~sci-libs/gdal { |
1091 |
@@ -30,37 +28,29 @@ sci-libs/gdal { |
1092 |
} |
1093 |
|
1094 |
sci-libs/gsl { |
1095 |
- gsl. Note: users should have GSL installed. Windowsusers: 'consult the README file available in the inst directoryof the source distribution for necessary configurationinstructions'. |
1096 |
- gsl (with development libraries) |
1097 |
+ ^gsl |
1098 |
} |
1099 |
~sci-libs/gsl { |
1100 |
GNU GSL |
1101 |
- gsl |
1102 |
+ ^gsl |
1103 |
libgsl |
1104 |
- libgslcblas |
1105 |
- GNU GSL for the GSL random-number generators |
1106 |
- GNU GSL forthe GSL random-number generators |
1107 |
- GNU Scientific Library (GSL) |
1108 |
- GNU Scientific Library version |
1109 |
+ GNU Scientific Library |
1110 |
} |
1111 |
|
1112 |
~sci-libs/hdf5 :: hdf5 |
1113 |
sci-libs/hdf5[cxx] { |
1114 |
- libhdf5 (>= 1.8.x) with C++ interface(--enable-cxx=yes) |
1115 |
- libhdf5 (>= 1.8.12) with C++ interface(--enable-cxx=yes) |
1116 |
+ libhdf5.*C\+\+ |
1117 |
} |
1118 |
# remnant of hdf5 |
1119 |
! :: v18 API enabled |
1120 |
|
1121 |
~sci-libs/itpp { |
1122 |
- itpp |
1123 |
- libitpp |
1124 |
+ itpp$ |
1125 |
} |
1126 |
|
1127 |
# FIXME: dev-lang/R[lapack]? |
1128 |
virtual/lapack { |
1129 |
- LAPACK sharedlibrary |
1130 |
- LAPACKshared library |
1131 |
+ LAPACK |
1132 |
} |
1133 |
|
1134 |
sci-libs/lapack-atlas :: lapack_atlas |
1135 |
@@ -70,19 +60,12 @@ sci-libs/libsvm :: SVMlight |
1136 |
|
1137 |
~sci-libs/mkl :: Intel MKL |
1138 |
|
1139 |
-sci-libs/netcdf :: netcdf library version 4.1 or later |
1140 |
~sci-libs/netcdf :: netcdf |
1141 |
|
1142 |
-sci-libs/proj :: proj 4.4.6 or higher (http://proj.maptools.org/) |
1143 |
->=sci-libs/proj-4.4.9 :: PROJ.4(proj >= 4.4.9) |
1144 |
- |
1145 |
+sci-libs/proj :: ^proj |
1146 |
|
1147 |
# FIXME, portage version is 2.1.21 |
1148 |
-sci-libs/udunits :: udunits (>= 1.11.7) or udunits2(>= 2.1.22) |
1149 |
-~sci-libs/udunits { |
1150 |
- udunits |
1151 |
- udunits-2 |
1152 |
-} |
1153 |
+sci-libs/udunits :: udunits |
1154 |
|
1155 |
virtual/blas :: blas |
1156 |
|
1157 |
|
1158 |
diff --git a/config/simple-deprules.d/selfdeps b/config/simple-deprules.d/selfdeps |
1159 |
deleted file mode 100644 |
1160 |
index 63e49bc..0000000 |
1161 |
--- a/config/simple-deprules.d/selfdeps |
1162 |
+++ /dev/null |
1163 |
@@ -1,22 +0,0 @@ |
1164 |
-#! NOPARSE |
1165 |
-#! ERROR |
1166 |
-# Replaced by the selfdeps.d directory, which contains per-repo selfdep files. |
1167 |
-# |
1168 |
-# This file lists old rules, which are not yet included there. |
1169 |
-# |
1170 |
- |
1171 |
-#deptype pkg,selfdep |
1172 |
- |
1173 |
-sci-R/chron :: get.hist.quote needs packagechron. |
1174 |
- |
1175 |
-# FIXME: correct? |
1176 |
-~sci-R/CoCo { |
1177 |
- CoCoCore |
1178 |
- CoCoObjects |
1179 |
- CoCoRaw |
1180 |
-} |
1181 |
-sci-R/survival4 :: survival4 if survival models are to be used. |
1182 |
-~sci-R/survival5 :: survival5 for some examples |
1183 |
-sci-R/survival5 :: survival5 if survival models are to be used. |
1184 |
- |
1185 |
-~sci-R/VhayuR :: Vhayu |
1186 |
|
1187 |
diff --git a/config/simple-deprules.d/selfdeps.d/sci-CRAN b/config/simple-deprules.d/selfdeps.d/sci-CRAN |
1188 |
index 5935939..0994353 100644 |
1189 |
--- a/config/simple-deprules.d/selfdeps.d/sci-CRAN |
1190 |
+++ b/config/simple-deprules.d/selfdeps.d/sci-CRAN |
1191 |
@@ -1,30 +1,29 @@ |
1192 |
#deptype pkg,selfdep |
1193 |
|
1194 |
sci-CRAN/csound { |
1195 |
- A valid copy of the Csound library must be present.Csound can be downloaded from http://www.csounds.com. Thelibrary is included in the default Windows and Mac OS Xdistributions |
1196 |
- playitbyr creates sound using the csound package |
1197 |
- which requires the free and open source software synthesizerCsound |
1198 |
+ Csound |
1199 |
} |
1200 |
|
1201 |
-~sci-CRAN/mimR :: mim |
1202 |
+# IRKernel has a conflicting named sci-R/repr. |
1203 |
+~sci-CRAN/repr :: ^repr$ |
1204 |
+ |
1205 |
+~sci-CRAN/mimR :: ^mim$ |
1206 |
|
1207 |
sci-CRAN/quadprog :: portfolio.optim needs package quadprog |
1208 |
|
1209 |
sci-CRAN/rgl :: rgl packages for rendering |
1210 |
|
1211 |
sci-CRAN/MVA { |
1212 |
- white.test needs packagemva |
1213 |
- white.test needs package mva |
1214 |
+ package.*mva |
1215 |
} |
1216 |
|
1217 |
~sci-CRAN/sgeostat { |
1218 |
- sgeostat. |
1219 |
- geostat. |
1220 |
+ geostat |
1221 |
} |
1222 |
|
1223 |
# the following rule is _not_ correct |
1224 |
-# (the dependency strings listed here want the "xgobi" program from |
1225 |
-# http://www.research.att.com/areas/stat/xgobi/, not the R package) |
1226 |
+# the dependency strings listed here want the "xgobi" program from |
1227 |
+# http://www.research.att.com/areas/stat/xgobi/, not the R package |
1228 |
# |
1229 |
## sci-CRAN/xgobi { |
1230 |
## xgobi must be installed additionally |
1231 |
@@ -33,8 +32,6 @@ sci-CRAN/MVA { |
1232 |
|
1233 |
~sci-CRAN/BayesFactor :: BayesFactorPCL |
1234 |
|
1235 |
->=sci-CRAN/adimpro-0.4.2 :: adimpro (>= 0.4.2)The R-package 'adimpro' (for reading |
1236 |
- |
1237 |
sci-CRAN/adimpro { |
1238 |
- The R-package 'adimpro' (for reading |
1239 |
+ adimpro |
1240 |
} |
1241 |
|
1242 |
diff --git a/config/simple-deprules.d/sys b/config/simple-deprules.d/sys |
1243 |
index b2fa9bd..88ddb06 100644 |
1244 |
--- a/config/simple-deprules.d/sys |
1245 |
+++ b/config/simple-deprules.d/sys |
1246 |
@@ -2,25 +2,19 @@ |
1247 |
|
1248 |
~sys-libs/db { |
1249 |
BerkelyDB |
1250 |
- BerkeleyDB |
1251 |
- Oracle Berkeley DB 11gR2 |
1252 |
+ Berkeley.*DB |
1253 |
} |
1254 |
|
1255 |
~sys-libs/zlib :: zlib |
1256 |
-sys-libs/zlib :: zlib (optional) |
1257 |
|
1258 |
# => sys-cluster/ |
1259 |
virtual/mpi { |
1260 |
- LamMPI(>= 6.5.9) or MPICH2(>= 1.0.2) or OpenMPI () |
1261 |
- LamMpi(>= 6.5.9) or Mpich2(>= 1.0.2) |
1262 |
- OpenMPI (>= 1.5.4) on Linux |
1263 |
- OpenMPI or MPICH2 |
1264 |
-} |
1265 |
- |
1266 |
-# the "... on Windows" line could probably be ignored |
1267 |
-virtual/mpi { |
1268 |
+ LamMPI |
1269 |
+ Open.*MPI |
1270 |
+ MPICH2 |
1271 |
MPI2 |
1272 |
- MPICH2 (>=1.4.1p1) on Windows |
1273 |
+ MPICH2 |
1274 |
+ MPI.*library |
1275 |
} |
1276 |
|
1277 |
! { |
1278 |
@@ -32,17 +26,15 @@ virtual/mpi { |
1279 |
~sci-R/Rcpp :: Rcpp |
1280 |
|
1281 |
# Split across multiple lines, next line adds Linux and Mac |
1282 |
->=sys-cluster/openmpi-1.5.4 :: OpenMPI (>= 1.5.4) on Solaris |
1283 |
+>=sys-cluster/openmpi-1.5.4 :: OpenMPI |
1284 |
|
1285 |
@selfdep |
1286 |
-sci-R/rJava :: JRI |
1287 |
- |
1288 |
-~app-text/pandoc :: Pandoc (http://johnmacfarlane.net/pandoc) forexporting markdown files to other formats. |
1289 |
+sci-R/rJava :: ^JRI$ |
1290 |
|
1291 |
->=dev-tcltk/tktable-2.9 :: Tktable (>= 2.9 |
1292 |
+~dev-tcltk/tktable :: Tktable |
1293 |
|
1294 |
->=app-text/aspell-0.60 :: aspell (>= 0.60 |
1295 |
+~app-text/aspell :: aspell |
1296 |
|
1297 |
-dev-libs/openssl :: OpenSSL library |
1298 |
+dev-libs/openssl :: OpenSSL |
1299 |
|
1300 |
-~app-crypt/dieharder :: DieHarder library |
1301 |
+~app-crypt/dieharder :: DieHarder |
1302 |
|
1303 |
diff --git a/config/simple-deprules.d/system.set b/config/simple-deprules.d/system.set |
1304 |
index 54fc6a5..1e9b3e8 100644 |
1305 |
--- a/config/simple-deprules.d/system.set |
1306 |
+++ b/config/simple-deprules.d/system.set |
1307 |
@@ -2,43 +2,26 @@ |
1308 |
|
1309 |
# @system |
1310 |
! { |
1311 |
+ bash |
1312 |
+ ^awk$ |
1313 |
+ gmake |
1314 |
GNU make |
1315 |
- GNU Make |
1316 |
- GNU Make forexternalization |
1317 |
- andg++ GNU compiler (a nvcc-compatible version of g++ is needed |
1318 |
- andg++ GNU compiler version 3.4 (version 4.4 is not yet compatiblewith nvcc). |
1319 |
- chmod) |
1320 |
-} |
1321 |
- |
1322 |
-% :: gcc |
1323 |
-# FIXME: newer gcc versions could work, too |
1324 |
-<sys-devel/gcc-4.4 :: gcc/g++ version 4.4 is not yet compatible with nvcc). |
1325 |
-<=sys-devel/gcc-4.5 :: gcc (release <= 4.5). |
1326 |
- |
1327 |
-#sys-devel/gcc[cxx] :: g++ or Microsoft VC++ |
1328 |
-! :: g++ or Microsoft VC++ |
1329 |
-! { |
1330 |
- g++-4.6.* or later should be sufficient |
1331 |
- g++-4.9.* or lateris preferred. |
1332 |
- gcc (release >= 4.5). |
1333 |
- C++11 |
1334 |
- C++11 (supporting at least std=c++0x) |
1335 |
- A C++11 compiler. Version 4.6.* of g++ (ascurrently in Rtools) is insufficient |
1336 |
+ g\+\+ GNU compiler |
1337 |
+ chmod |
1338 |
+ ^gcc |
1339 |
+ ^g\+\+ |
1340 |
+ ^C\+\+11 |
1341 |
+ C\+\+11.*compiler |
1342 |
} |
1343 |
|
1344 |
# always provided? (except for Gentoo/*BSD) |
1345 |
! { |
1346 |
- Linux operating system |
1347 |
- Linux operating system. |
1348 |
- Linuxoperationg system |
1349 |
+ Linux.*operating.*system |
1350 |
} |
1351 |
# always provided |
1352 |
! { |
1353 |
- POSIX-compliant OS (essentially anything but Windows) |
1354 |
- POSIX-compliant OS (essentially anything butWindows |
1355 |
- POSIX-compliant OS (essentially anything butWindows) |
1356 |
+ POSIX.*OS |
1357 |
Unix |
1358 |
- A 64-bit POSIX OS such as Linux or OS X with IANAtime zone data in /usr/share/zoneinfo as well as a C++11compiler. |
1359 |
} |
1360 |
|
1361 |
# rpcgen is part of glibc |
1362 |
|
1363 |
diff --git a/config/simple-deprules.d/unknown b/config/simple-deprules.d/unknown |
1364 |
index 8d1549d..04d20b6 100644 |
1365 |
--- a/config/simple-deprules.d/unknown |
1366 |
+++ b/config/simple-deprules.d/unknown |
1367 |
@@ -2,7 +2,6 @@ |
1368 |
|
1369 |
# FIXME: which library is meant? |
1370 |
! { |
1371 |
- A C library with the fesetround/fegetroundfunctions. |
1372 |
- library. |
1373 |
- library |
1374 |
+ ^C.*library |
1375 |
+ ^library |
1376 |
} |
1377 |
|
1378 |
diff --git a/config/simple-deprules.d/x11 b/config/simple-deprules.d/x11 |
1379 |
index 2858ddd..ff93d39 100644 |
1380 |
--- a/config/simple-deprules.d/x11 |
1381 |
+++ b/config/simple-deprules.d/x11 |
1382 |
@@ -1,26 +1,22 @@ |
1383 |
#deptype sys |
1384 |
|
1385 |
-x11-libs/cairo :: cairo (>= 1.2 http://www.cairographics.org/) |
1386 |
~x11-libs/cairo :: cairo |
1387 |
|
1388 |
-~x11-libs/gtk+ :: gtk+ |
1389 |
+~x11-libs/gtk+ :: gtk\+ |
1390 |
|
1391 |
~x11-libs/pango :: pango |
1392 |
|
1393 |
# qt has its own category now |
1394 |
dev-qt/qtcore { |
1395 |
- qt |
1396 |
- Qt4 libraries and headers (http://qt.nokia.com) |
1397 |
- Qt4 libraries |
1398 |
+ ^qt$ |
1399 |
+ ^Qt4.*libraries |
1400 |
} |
1401 |
-! :: headers (http://qt.nokia.com) |
1402 |
|
1403 |
x11-misc/xclip { |
1404 |
- xclip (Linux) |
1405 |
+ xclip |
1406 |
} |
1407 |
|
1408 |
virtual/opencl { |
1409 |
- OpenCL library |
1410 |
OpenCl |
1411 |
} |
1412 |
|
1413 |
|
1414 |
diff --git a/roverlay/depres/simpledeprule/abstractrules.py b/roverlay/depres/simpledeprule/abstractrules.py |
1415 |
index d31ffbe..a1d8522 100644 |
1416 |
--- a/roverlay/depres/simpledeprule/abstractrules.py |
1417 |
+++ b/roverlay/depres/simpledeprule/abstractrules.py |
1418 |
@@ -8,7 +8,7 @@ |
1419 |
|
1420 |
__all__ = [ 'FuzzySimpleRule', 'SimpleRule', ] |
1421 |
|
1422 |
-import logging |
1423 |
+import logging, re |
1424 |
|
1425 |
from roverlay import config |
1426 |
from roverlay.depres import deprule |
1427 |
@@ -21,7 +21,7 @@ class SimpleRule ( deprule.DependencyRule ): |
1428 |
INDENT = 3 * ' ' |
1429 |
|
1430 |
def __init__ ( self, |
1431 |
- dep_str=None, priority=50, resolving_package=None, |
1432 |
+ dep_str=None, priority=80, resolving_package=None, |
1433 |
is_selfdep=0, logger_name='simple_rule', |
1434 |
selfdep_package_names=None, finalize=False, |
1435 |
): |
1436 |
@@ -67,6 +67,10 @@ class SimpleRule ( deprule.DependencyRule ): |
1437 |
self.dep_alias = frozenset ( self.dep_alias ) |
1438 |
if self.prepare_lowercase_alias: |
1439 |
self.dep_alias_low = frozenset ( x.lower() for x in self.dep_alias ) |
1440 |
+ temp_set = self.dep_alias_low |
1441 |
+ if self.is_selfdep: |
1442 |
+ temp_set = ("^{}$".format(x) for x in self.dep_alias_low) |
1443 |
+ self.dep_regex = re.compile('|'.join(x for x in temp_set)) |
1444 |
|
1445 |
def add_resolved ( self, dep_str ): |
1446 |
"""Adds an dependency string that should be matched by this rule. |
1447 |
@@ -80,7 +84,7 @@ class SimpleRule ( deprule.DependencyRule ): |
1448 |
def _find ( self, dep_str, lowercase ): |
1449 |
if lowercase: |
1450 |
if hasattr ( self, 'dep_alias_low' ): |
1451 |
- if dep_str in self.dep_alias_low: |
1452 |
+ if self.dep_regex.search(dep_str): |
1453 |
return True |
1454 |
|
1455 |
elif dep_str in ( alias.lower() for alias in self.dep_alias ): |
1456 |
|
1457 |
diff --git a/roverlay/depres/simpledeprule/rules.py b/roverlay/depres/simpledeprule/rules.py |
1458 |
index 869c5aa..12c6520 100644 |
1459 |
--- a/roverlay/depres/simpledeprule/rules.py |
1460 |
+++ b/roverlay/depres/simpledeprule/rules.py |
1461 |
@@ -151,11 +151,11 @@ class SimpleIgnoreDependencyRule ( SimpleRule ): |
1462 |
|
1463 |
RULE_PREFIX = '!' |
1464 |
|
1465 |
- def __init__ ( self, priority=50, resolving_package=None, **kw ): |
1466 |
+ def __init__ ( self, priority=80, resolving_package=None, **kw ): |
1467 |
super ( SimpleIgnoreDependencyRule, self ) . __init__ ( |
1468 |
logger_name = 'IGNORE_DEPS', |
1469 |
resolving_package=None, |
1470 |
- priority=50, |
1471 |
+ priority=80, |
1472 |
**kw |
1473 |
) |
1474 |
# --- end of SimpleIgnoreDependencyRule --- |
1475 |
@@ -187,7 +187,7 @@ class SimpleFuzzyIgnoreDependencyRule ( FuzzySimpleRule ): |
1476 |
|
1477 |
RULE_PREFIX = '%' |
1478 |
|
1479 |
- def __init__ ( self, priority=51, resolving_package=None, **kw ): |
1480 |
+ def __init__ ( self, priority=81, resolving_package=None, **kw ): |
1481 |
super ( SimpleFuzzyIgnoreDependencyRule, self ) . __init__ ( |
1482 |
priority=priority, |
1483 |
resolving_package=resolving_package, |