From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 33EDF13800E for ; Mon, 30 Jul 2012 08:55:12 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 45173E072E; Mon, 30 Jul 2012 08:52:57 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id E5943E0720 for ; Mon, 30 Jul 2012 08:52:56 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C13F31B4008 for ; Mon, 30 Jul 2012 08:52:49 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 114C0E5454 for ; Mon, 30 Jul 2012 08:52:47 +0000 (UTC) From: "André Erdmann" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "André Erdmann" Message-ID: <1343638111.e5fc16a751755b9de646d1a2b5b1a7d8016c6e4a.dywi@gentoo> Subject: [gentoo-commits] proj/R_overlay:master commit in: simple-deprules.d/ X-VCS-Repository: proj/R_overlay X-VCS-Files: simple-deprules.d/R simple-deprules.d/app simple-deprules.d/app-text simple-deprules.d/compound_deps simple-deprules.d/dev simple-deprules.d/dev-libs simple-deprules.d/dot_remap simple-deprules.d/gnome simple-deprules.d/ignored_text simple-deprules.d/media simple-deprules.d/media-libs simple-deprules.d/missing simple-deprules.d/net simple-deprules.d/nvidia simple-deprules.d/other simple-deprules.d/perl simple-deprules.d/sci simple-deprules.d/sci-libs simple-deprules.d/selfdeps simple-deprules.d/sys simple-deprules.d/system.set simple-deprules.d/unknown simple-deprules.d/x11 X-VCS-Directories: simple-deprules.d/ X-VCS-Committer: dywi X-VCS-Committer-Name: André Erdmann X-VCS-Revision: e5fc16a751755b9de646d1a2b5b1a7d8016c6e4a X-VCS-Branch: master Date: Mon, 30 Jul 2012 08:52:47 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: ed623f1e-739e-4857-ad46-afa26c40df63 X-Archives-Hash: f2607cf9d491a3de1a0c37902d0feff7 commit: e5fc16a751755b9de646d1a2b5b1a7d8016c6e4a Author: André Erdmann mailerd de> AuthorDate: Mon Jul 30 08:48:31 2012 +0000 Commit: André Erdmann mailerd de> CommitDate: Mon Jul 30 08:48:31 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=e5fc16a7 dependency rules --- simple-deprules.d/R | 51 +++++++- simple-deprules.d/app | 12 ++ simple-deprules.d/app-text | 20 +++ simple-deprules.d/compound_deps | 49 +++++++ simple-deprules.d/dev | 43 ++++++ simple-deprules.d/dev-libs | 57 ++++++++ simple-deprules.d/dot_remap | 72 ++++++++++ simple-deprules.d/gnome | 5 + simple-deprules.d/ignored_text | 58 ++++++++ simple-deprules.d/media | 22 +++ simple-deprules.d/media-libs | 42 ++++++ simple-deprules.d/missing | 296 +++++++++++++++++++++++++++++++++++++++ simple-deprules.d/net | 24 +++ simple-deprules.d/nvidia | 27 ++++ simple-deprules.d/other | 1 - simple-deprules.d/perl | 12 ++ simple-deprules.d/sci | 53 +++++++ simple-deprules.d/sci-libs | 73 ++++++++++ simple-deprules.d/selfdeps | 60 +++++++- simple-deprules.d/sys | 16 ++ simple-deprules.d/system.set | 30 ++++ simple-deprules.d/unknown | 6 + simple-deprules.d/x11 | 25 ++++ 23 files changed, 1043 insertions(+), 11 deletions(-) diff --git a/simple-deprules.d/R b/simple-deprules.d/R index 0bdba02..ac8c3d4 100644 --- a/simple-deprules.d/R +++ b/simple-deprules.d/R @@ -1,8 +1,55 @@ +#deptype all + # R versions available in portage: # 2.10.1, 2.14.1, 2.14.2, 2.15.0, 2.15.1 -# R is always compiled with '--enabled-R-shlib'; from: 'Rserve_0.6.8' -! :: R must be compiled with --enable-R-shlib if the server is to be built +#deptype all # using fuzzy dep matches ~dev-lang/R :: R + +dev-lang/R[tk] { + tcl/tk 8.5 + Tcl/Tk (>= 8.5) + tcltk (but only for the GUI +} + +# always assumed to be provided by dev-lang/R (taken from generate_ebuild) +% { + base + compiler + datasets + graphics + grDevices + grid + methods + parallel + splines + stats + stats4 + tcltk + tools + utils +} +# FIXME, seems to be provided too +% { + stepfun + ts + package ts + package ts (included in the R release) +} +# modreg is in stats, according to https://stat.ethz.ch/pipermail/bioconductor/2010-June/034197.html +! :: modreg + +# R is always compiled with '--enabled-R-shlib' +! { + R must be compiled with --enable-R-shlib if the server is to be built + R must be compiled with --enable-R-shlib if theserver is to be built + Download regular shlib (420 KB) from externalsource ('xls.getshlib()' or manually) + R built as a shared object + R built as a shared or static (R >= 2.7.0) library + R built as a shared orstatic library + R-0.64 or later + Regular shlib must be obtained from an externalsource (use 'xls.getshlib()' or dl manually). + dl regular shlib with 'xls.getshlib()'or manually (~420 KB) +} diff --git a/simple-deprules.d/app b/simple-deprules.d/app new file mode 100644 index 0000000..99ba3c3 --- /dev/null +++ b/simple-deprules.d/app @@ -0,0 +1,12 @@ +#deptype sys + +app-admin/ec2-api-tools :: ec2-api-tools + +# FIXME zip or unzip? +app-arch/zip :: zip + +# FIXME: this is not satisfiable, latest dieharder version in portage is 2.28.1 +app-crypt/dieharder { + DieHarder library (>= 2.8.1) fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php + DieHarder library (>= 3.31.1) fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php +} diff --git a/simple-deprules.d/app-text b/simple-deprules.d/app-text new file mode 100644 index 0000000..3d1a579 --- /dev/null +++ b/simple-deprules.d/app-text @@ -0,0 +1,20 @@ +#deptype sys + +app-text/antiword { + Antiword (http://www.winfield.demon.nl/) forreading MS Word files + antiword for reading MS Word files +} + +~app-text/ghostscript-gpl :: ghostscript + +app-text/poppler { + pdfinfo andpdftotext for reading PDF + pdfinfo and pdftotext from Poppler(http://poppler.freedesktop.org/) for reading PDF + pdftotext from Poppler(http://poppler.freedesktop.org/) for reading PDF +} + +# pdflatex? +app-text/texlive { + (PDF)LaTeX (http://www.latex-project.org/) withpdfpages package for studentGrowthPlot option in visualizeSGPto bind together student growth plots into school catalogs. + (PDF)LaTeX for saveLatex() +} diff --git a/simple-deprules.d/compound_deps b/simple-deprules.d/compound_deps new file mode 100644 index 0000000..fa88ae7 --- /dev/null +++ b/simple-deprules.d/compound_deps @@ -0,0 +1,49 @@ +#deptype sys + +( media-libs/fontconfig media-fonts/corefonts ) { + fontconfig and msttcorefonts + fontconfig and msttcorefonts recommended) +} + +( net-libs/liboauth net-misc/curl ) { + liboauth (>= 0.9.4) liboauth.sourceforge.net andlibcurl http://curl.haxx.se +} + +# FIXME +( sci-libs/blas-atlas dev-util/nvidia-cuda-toolkit ) { + Atlas development build as well as a Nvidia GPU withCUDA support +} + +|| ( dev-libs/libxml2 dev-libs/expat ) { + Daniel Veillard's libxml(ftp://ftp.gnome.org/pub/GNOME/sources/libxml/)and/orJim Clark's expat (http://www.jclark.com/xml) + Daniel Veillard's libxml(ftp://ftp.gnome.org/pub/GNOME/stable/sources/libxml/)and/orJim Clark's expat (http://www.jclark.com/xml) +} + +( media-libs/tiff >=sci-libs/fftw-3 ) { + optional libtiff and fftw3 +} + +( sci-libs/gdal sci-libs/proj ) { + for building from source: GDAL >= 1.3.1 && GDAL < 1.6.0 (until tested) library from http://www.gdal.org/download.html and PROJ.4 (proj >= 4.4.9) from http://proj.maptools.org/ + for building from source: GDAL >= 1.3.1 library from http://trac.osgeo.org/gdal/wiki/DownloadSource and PROJ.4 (proj >= 4.4.9) from http://trac.osgeo.org/proj/ + for building from source: GDAL >= 1.3.1 libraryfrom http://trac.osgeo.org/gdal/wiki/DownloadSource and PROJ.4(proj >= 4.4.9) from http://trac.osgeo.org/proj/ + for building from source: GDAL >= 1.3.1 library from http://www.gdal.org/download.html and PROJ.4 (proj >= 4.4.9) from http://proj.maptools.org/ + for building from source: GDAL >= 1.3.1 library from http://www.gdal.org/download.html and PROJ.4 (proj >= 4.4.9) from http://www.remotesensing.org/proj/ + for building from source: GDAL >= 1.6.0 libraryfrom http://trac.osgeo.org/gdal/wiki/DownloadSource and PROJ.4(proj >= 4.4.9) from http://trac.osgeo.org/proj/ +} + +( dev-libs/mpfr dev-libs/gmp ) { + http://mpfr.org/) and GMP (GNU Multiple Precision library +} + +|| ( media-gfx/imagemagick media-gfx/graphicsmagick ) { + ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) for saveGIF() +} + +|| ( media-gfx/imagemagick media-gfx/graphicsmagick app-office/lyx ) { + ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) or LyX(http://www.lyx.org) for saveGIF() +} + +|| ( media-libs/tiff virtual/jpeg ) { + libtiff and/or libjpeg +} diff --git a/simple-deprules.d/dev b/simple-deprules.d/dev new file mode 100644 index 0000000..9c256e8 --- /dev/null +++ b/simple-deprules.d/dev @@ -0,0 +1,43 @@ +#deptype sys + +dev-cpp/gtkmm :: gtkmm-2.4 + +~dev-db/mongodb :: mongodb + +# FIXME: dev-db/postgresql-server ? +~dev-db/postgresql-base { + PostgreSql +} + +# FIXME +dev-db/unixODBC { + An ODBC driver manager and drivers. See README. + An ODBC3 driver manager and drivers. + An ODBC3 driver manager and drivers. See README. + ODBC support and a back end database +} + +dev-java/ant :: ant +dev-java/jdbc-postgresql:: PostgreSQL JDBCdriver + +# lowest python version in portage: 2.5 +~dev-lang/python :: python +dev-lang/lua :: lua version>= 5.1.4 +~dev-lang/lua :: lua + +~dev-tex/pgf :: pgf + +dev-tcltk/bwidget :: bwidget +~dev-tcltk/tktable :: tktable + +dev-util/cmake { + cmake + cmake (http://www.cmake.org) +} + +~virtual/jdk { + java + Java 1.4 or later + Java version + java runtime +} diff --git a/simple-deprules.d/dev-libs b/simple-deprules.d/dev-libs new file mode 100644 index 0000000..fadc63b --- /dev/null +++ b/simple-deprules.d/dev-libs @@ -0,0 +1,57 @@ +#deptype sys + +~dev-libs/atk :: ATK + +dev-libs/boost { + Boost + Boost C++ libraries (1.31 or greater) + Boost library (>= 1.34.0) from http://www.boost.org + Boost library (>= 1.34.0) fromhttp://www.boost.org + Boost library from http://www.boost.org + Boost libraryfrom http://www.boost.org + boost headers for smart pointers + The Boost 'program_options' library(http://boost.org) is required. +} + +~dev-libs/glib :: glib + +~dev-libs/gmp { + libgmp + gmp +} +~dev-libs/gmp { + GMP (GNU MP bignum library from http://gmplib.org/) + GMP (GNU MP bignum library) + GMP (GNU Multiple Precision library + http://gmplib.org/) +} + +~dev-libs/libxml2 :: libxml2 + +~dev-libs/libxslt :: libxslt + +dev-libs/mpc { + and MPC (Multiple Precision ComplexLibrary + http://www.multiprecision.org/) +} + +~dev-libs/mpfr { + MPFR (MP Floating-Point Reliable Library + mpfr + http://mpfr.org/) +} +# FIXME versions -> fuzzy +dev-libs/quantlib { + QuantLib libraries must be installed + QuantLib library (>= 0.8.1) from http://quantlib.org + QuantLib library (>= 0.9.0) from http://quantlib.org + QuantLib library (>= 0.9.7) from http://quantlib.org + QuantLib library (>= 0.9.7) fromhttp://quantlib.org + QuantLib library (>= 0.9.9) fromhttp://quantlib.org + QuantLib library from http://quantlib.org +} + +~dev-libs/xerces-c { + xerces-c + libxerces-c +} diff --git a/simple-deprules.d/dot_remap b/simple-deprules.d/dot_remap new file mode 100644 index 0000000..57d65b1 --- /dev/null +++ b/simple-deprules.d/dot_remap @@ -0,0 +1,72 @@ +#deptype pkg + +~sci-R/aroma_affymetrix :: aroma.affymetrix +~sci-R/aroma_apd :: aroma.apd +~sci-R/aroma_core :: aroma.core +~sci-R/aroma_light :: aroma.light + +~sci-R/bio_infer :: bio.infer + +~sci-R/Ckmeans_1d_dp :: Ckmeans.1d.dp +~sci-R/clim_pact :: clim.pact +~sci-R/compute_es :: compute.es +~sci-R/conf_design :: conf.design + +~sci-R/data_table :: data.table +~sci-R/DoE_base :: DoE.base +~sci-R/DoE_wrapper :: DoE.wrapper + +~sci-R/ergm_userterms :: ergm.userterms + +~sci-R/FrF2_catlg128 :: FrF2.catlg128 +~sci-R/FunciSNP :: FunciSNP.data +~sci-R/futile_any :: futile.any +~sci-R/futile_logger :: futile.logger +~sci-R/futile_matrix :: futile.matrix +~sci-R/futile_options :: futile.options +~sci-R/futile_paradigm :: futile.paradigm + +~sci-R/gamlss_data :: gamlss.data +~sci-R/gamlss_dist :: gamlss.dist +~sci-R/gamlss_nl :: gamlss.nl +~sci-R/gamlss_tr :: gamlss.tr +~sci-R/gamlss_util :: gamlss.util +~sci-R/GO_db :: GO.db + +~sci-R/haplo_score :: haplo_score +~sci-R/haplo_stats :: haplo_stats +~sci-R/heapmap_plus :: heatmap.plus + +~sci-R/lava_tobit :: lava.tobit + +~sci-R/minpack_lm :: minpack.lm + +~sci-R/opencpu_encode :: opencpu.encode +~sci-R/openNLPmodels_en :: openNLPmodels.en +~sci-R/openNLPmodels_es :: openNLPmodels.es +~sci-R/operator_tools :: operator.tools +~sci-R/orloca_es :: orloca.es +~sci-R/oro_dicom :: oro.dicom +~sci-R/oro_nifti :: oro.nifti + +~sci-R/R_cache :: R.cache +~sci-R/RcmdrPlugin_IPSUR :: RcmdrPlugin.IPSUR +~sci-R/R_devices :: R.devices +~sci-R/R_filesets :: R.filesets +~sci-R/R_huge :: R.huge +~sci-R/R_matlab :: R.matlab +~sci-R/R_methodsS3 :: R.methodsS3 +~sci-R/ROI_plugin_glpk :: ROI.plugin.glpk +~sci-R/ROI_plugin_quadprog :: ROI.plugin.quadprog +~sci-R/ROI_plugin_symphony :: ROI.plugin.symphony +~sci-R/R_oo :: R.oo +~sci-R/rpart_plot :: rpart.plot +~sci-R/R_rsp :: R.rsp +~sci-R/RSQLite_extfuns :: RSQLite.extfuns +~sci-R/R_utils :: R.utils + +~sci-R/Sim_DiffProc :: Sim.DiffProc +~sci-R/SNPMaP_cdm :: SNPMaP.cdm +~sci-R/survJamda_data :: survJamda.data + +~sci-R/tawny_types :: tawny.types diff --git a/simple-deprules.d/gnome b/simple-deprules.d/gnome new file mode 100644 index 0000000..1e85243 --- /dev/null +++ b/simple-deprules.d/gnome @@ -0,0 +1,5 @@ +#deptype sys + +~gnome-base/libglade :: libglade + +gnome-base/libgnome :: GNOME development libraries diff --git a/simple-deprules.d/ignored_text b/simple-deprules.d/ignored_text new file mode 100644 index 0000000..909e028 --- /dev/null +++ b/simple-deprules.d/ignored_text @@ -0,0 +1,58 @@ +#deptype all + +# ignored text +! { + available at . See for more guidance on settingup Csound. + available at. This package uses the sharedlibrary file + becauseBRugs does not support other platforms/OS right now. + binary Linux distributions often package thelibrary separately from the executible file + it is an extension for the R package tcltk that consists of Tclscripts. See README file. + all other functions are stand alone) + see also the topic 'SoPhy' in the documentation + see also the topic'SoPhy' in the documentation + see file README + see README + see README. + see ./README. + see the cloudRmpi manual (vignette)for details. + see topic SoPhy below + so for instance onDebian and Ubuntu you would need the "libcsound64-dev" package.See the package web site for more guidance on setup andconfiguration. + so for instance onDebian and Ubuntu you would need the "libcsound64-dev" package.See the web site below for more guidance on setup. + some Windows variants are supported experimentally + your mileage may vary) + optional) + heavily suggested) + hence Windows or Linux + $distributions package thelibrary file separately from the executible + or INSTALL.windows under Windows + standard unix tools (e.g. + rgdal OSX binary packages are also available at the samesite. + rgdal OSX binary packages are also available at the same site. +} + +! :: None + +! { + Will use djmrgl or rgl packages for rendering ifpresent + Will use djmrgl or rgl packages for rendering if present + SYMPHONY for Windows (sources included for otherOSes) +} + +# ignore OSX recommendations +! { + GDAL OSX frameworks built by William Kyngesburye at http://www.kyngchaos.com/ may be used for source installs on OSX + GDAL OSXframeworks built by William Kyngesburye athttp://www.kyngchaos.com/ may be used for source installs onOSX + GDAL OSXframeworks built by William Kyngesburye athttp://www.kyngchaos.com/ may be used for source installs onOSX. +} + +! { + GEOS OSX frameworks built byWilliam Kyngesburye at http://www.kyngchaos.com/ may be usedfor source installs on OSX. +} + +# SoPhy splits its Depends field into windows and linux +! { + windows:Tiff for windows + windows: Tiff (libtiff3.dll) + windows: Tiff(libtiff3.dll) + zlib1.dll and jpeg62.dll +} diff --git a/simple-deprules.d/media b/simple-deprules.d/media new file mode 100644 index 0000000..5692eac --- /dev/null +++ b/simple-deprules.d/media @@ -0,0 +1,22 @@ +#deptype sys + +~media-sound/csound :: csound + +~media-gfx/imagemagick :: imagemagick + +media-gfx/graphviz :: dot from graphviz +~media-gfx/graphviz { + graphviz + graphviz version +} + +media-gfx/swftools { + SWF Tools (http://swftools.org) forsaveSWF() + SWF Tools (http://swftools.org) for saveSWF() +} + +virtual/ffmpeg { + FFmpeg (http://ffmpeg.org) for saveVideo() + FFmpeg(http://ffmpeg.org) for saveVideo() + ffmpeg +} diff --git a/simple-deprules.d/media-libs b/simple-deprules.d/media-libs new file mode 100644 index 0000000..6558f40 --- /dev/null +++ b/simple-deprules.d/media-libs @@ -0,0 +1,42 @@ +#deptype sys + +~media-libs/flac :: flac + +# FIXME: some packages write optional deps into SystemRequirements (e.g. rgl from CRAN) +media-libs/freetype :: FreeType (optional) +~media-libs/freetype :: freetype +media-libs/freetype:2 :: recommended: freetype2 + +media-libs/gd { + libgd (>= 2.0.28 http://www.boutell.com/gd/) + libgd (>= 2.0.29 http://www.boutell.com/gd/) + libgd (freetype2 +} + +media-libs/libpng { + libpng(>=1.2.9 + libpng (optional) + libpng(optional) +} +~media-libs/libpng { + png + libpng +} + +~media-libs/libsndfile :: libsndfile + +~media-libs/netpbm :: netpbm + +media-libs/raptor :: libraptor2 (>= 2.0.0 http://librdf.org/raptor/) + +media-libs/tiff :: linux: libtiff (and libtiff-devel) +~media-libs/tiff { + tiff + libtiff + libtiff-devel +} + +virtual/jpeg { + libjpeg + jpeg +} diff --git a/simple-deprules.d/missing b/simple-deprules.d/missing new file mode 100644 index 0000000..0cf60b4 --- /dev/null +++ b/simple-deprules.d/missing @@ -0,0 +1,296 @@ +#! NOPARSE + +# === Notes === + +* BIOC experimental -> these packages could also be included in BIOC-2.10; +-> solution: try BIOC-2.10 (next test run) + +* some packages have multiple 'Depends' fields which results in + dep strings like 'R (>= 2.3.0)Depends: tcltk' - fix this + +* maybe add dev-lang/R with specific USE flags to deps like lapack + +* omegahat? + + +# === missing === +ALL +ALLMLL +ActiveTcl +AffymetrixDataTestFiles -- BIOC experimental +AmpAffyExample -- BIOC experimental +ArcGIS -- seems to be some proprietary software for windows (which implies that a packages has incorrect OS_type set when reching depres) +BLACS -- not in portage, http://www.netlib.org/blacs/ +CCl4 -- BIOC experimental +CLL -- BIOC experimental +Currently only MS-WIndows OS is supported.* -- result of missing/incorrect OS_type in an R package +COIN-OR Clp -- not in portage, http://www.coin-or.org/projects/ +CodeDepends -- http://www.omegahat.org/CodeDepends/ +Concorde -- http://www.tsp.gatech.edu/concorde/ +Cytoscape -- http://www.cytoscape.org/, LPGL but wants some information from downloaders +DLBCL -- BIOC experimental +Do.db -- BIOC experimental +DSA -- partDSA from CRAN? +Goto Blas -- http://www.csar.cfs.ac.uk/user_information/software/maths/goto.shtml? +EatonEtAlChIPseq -- BIOC 2.10 +Windows -- see Currently... +Excel -- +FDb.UCSC.tRNAs -- BIOC 2.10 +FEAR -- suggested by Benchmarking from CRAN +File::Basename; File::Glob -- what's the correct perl dependency? +MERLIN -- http://www.sph.umich.edu/csg/abecasis/merlin/ +GAPS-JAGS -- described in http://www.rits.onc.jhmi.edu/dbb/custom/A6/Software/CoGAPSDistribution_v1_0/CoGAPSUsersManual.pdf +GGdata -- BIOC 2.10 +GO -- dev-lang/go, sys-devel/gcc[go], sci-R/GO_db, ...? +GSVAdata -- BIOC 2.10 +HEEBOdata -- BIOC 2.10 +HaarSeg -- http://webee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm +Hadoop -- http://hadoop.apache.org/core/ +Hive -- http://hive.apache.org/ +HuExExonProbesetLocation -- BIOC 2.10 +IBGEPesq -- ? +IBM ILOG CPLEX -- http://www-01.ibm.com/software/integration/optimization/cplex-optimizer/ +ITALICSData -- BIOC +IlluminaHumanMethylation** -- BIOC +Img -- (tcl/tk related?) +Internal files Xba.CQV -- ? +JRI -- java-related? (deducer from CRAN, openstreetmap from CRAN) +KEGG -- BIOC +Komodo Edit -- http://www.openkomodo.com +LAM MPI -- ? +MPI2 -- ? +Linux/64bit -- KEYWORD, not DEPEND!! +MAGMA shared libraries -- http://icl.cs.utk.edu/magma/software/index.html +MAQCsubset -- BIOC +MEEBOdata -- BIOC +MOSEK -- http://mosek.com/products/mosek/ +Mac OS X -- see Windows / Currently only Windows.. +MoExExonProbesetLocation -- BIOC +NMMAPSdata -- http://www.ihapss.jhsph.edu/data/NMMAPS/R/ ? +OpenBUGS -- http://www.openbugs.info/w/ +Oracle Instant Client or Oracle Database Client, Oracle client -- sys-libs/db +PREDAsampledata -- BIOC +PVM -- http://www.csm.ornl.gov/pvm/ +PWMEnrich.Dmelanogaster.background -- BIOC +Platform LSF development libraries -- ? +PolyPhen.Hsapiens.dbSNP131 -- BIOC +Protocol Buffer compiler (to create C++ header andsource files from .proto descriptions) and library (version2.2.0 or later) -- dev-libs/protobuf +RDCOMClient -- http://www.omegahat.org/RDCOMClient/ ==> maybe add omegahat as repo? +RGTK -- http://www.omegahat.org/RGtk/ +RaExExonProbesetLocation -- BIOC +Rcompression -- OmegaHat +Rcpp as sysdep (pcaMethods from BIOC) -- ? +"TODO!!!" -- sysdeps for svDialogs from CRAN; solution: deps unknown -> fail at ebuild creation +Win 32-bit -- Windows +affycompData -- BIOC +affydata -- BIOC +SPRNG -- http://sprng.cs.fsu.edu/ +asreml[-R] -- http://www.vsni.co.uk/downloads/asreml +beadarrayExampleData -- BIOC +bio3d -- http://mccammon.ucsd.edu/~bgrant/bio3d/download/download.html +bladderbatch -- BIOC +we expect to support Linux in future releases -- that's great, but why is it in DEPEND? +weexpect to support Linux in future releases -- ^ +XMLRPC -- what's the correct dep here? +breastCancerMAINZ, +breastCancerNKI, +breastCancerTRANSBIG, +breastCancerUNT, +breastCancerUPP, +breastCancerVDX -- BIOC +golubEsets -- BIOC +genomewidesnp5Crlmm -- BIOC +hgfocuscdf, +hgu133acdf, +hgu133afrmavecs, +hgu133aprobe, +hgu133atagcdf, +hgu133atagprobe, +hgu133plus2cdf, +hgu133plus2.db, +hgu133plus2probe, +hgu95acdf, +hgu95av2, +hgu95av2cdf, +hgu95av2cdf (>= 2.0.0), +hgu95av2.db, +hgu95av2.db (>= 1.13.0), +hgu95av2probe, +hgu95av2probe (>= 2.0.0), +hu6800, +hu6800.db, +hu6800.db (>= 1.8.1), +human370v1cCrlmm, +human610quadv1bCrlmm, +humanCHRLOC, +humanStemCell, +illuminaHumanv1.db, +illuminaHumanv3.db, +iontreeData -- BIOC +WinBUGS -- Windows only? +WinEdit -- ^ +tensor -- ? +expectile -- ? (required for aroma.core et al) +estrogen -- BIOC +ecolicdf, +ecoliLeucine, +faahKO -- BIOC +fEcofin -- "could" be in CRAN, to check; https://www.rmetrics.org/ +libsbml -- in portage?; http://sbml.org/Software/libSBML +ppiData -- BIOC +polynomial -- polynom? +Sxslt -- omegahat +yeastCC, +yeastExpData, +yeastNagalakshmi, +yeastRNASeq -- BIOC +statconnDCOM -- http://rcom.univie.ac.at/download.html#statconnDCOM +stdjudem -- BIOC +survnnet -- ? +SVGAnnotation -- omegahat +SuperCurve -- http://bioinformatics.mdanderson.org/Software/supercurve/ or OOMPA repo +gada - R-Forge? +gageData -- BIOC +mpcbs -- R-Forge +msdata -- BIOC +bsseqData, +charmData, +cMap, +cnvGSAdata, +colonCA -- BIOC +coefplot2 -- R-Forge +cudaMatrixOps -- cuda-toolkit? +dChipIO -- ? +hapmap100kxba, +hapmapsnp5, +hapmapsnp6 -- BIOC +iWidgets -- R-forge? +kopls -- http://kopls.sourceforge.net/ +pasillaBamSubset, pasilla -- BIOC +plasmodiumanophelescdf -- BIOC +rmutil -- http://www.commanster.eu/rcode.html +Vennerable -- R-Forge +test3cdf, +tweeDEseqCountData, +synapterdata, +SpikeInSubset, +snpMatrix, +simpIntLists, +serumStimulation, +RnaSeqTutorial, +rheumaticConditionWOLLBOLD, +rae230aprobe, +rat2302.db, +pumadata, +TargetSearchData -- BIOC +UScensus2000blk -- ? +spacemakeR -- R-Forge +sfit -- R package, but where to get? +ScaLAPACK -- http://www.netlib.org/scalapack/ +SAGA, SAGA-GIS -- http://www.saga-gis.org/en/index.html +rpcgen -- not in portage +SGE ?~ (qsub, qstat, optionally qacct) -- +reposTools -- BIOC +Rdonlp2 -- R-Forge +pdf2 -- ? +pairseqsim -- BIOC +oligoData -- BIOC +manipulate -- ? +drosgenome1.db, +drosophila2probe, +dyebiasexamples, +ffpeExampleData, +fibroEset, +flowWorkspaceData, +frmaExampleData, +gatingMLData, +gcspikelite, +geneLenDataBase, +leeBamViews, +lumiBarnes, +lumiHumanIDMapping, +lungExpression, +maqcExpression4plex, +minfiData, +moe430a, +mosaicsExample, +mouse4302.db, +mvoutData -- BIOC +lippthread -- ? +nwPro -- ? http://nws-r.sourceforge.net/ +nlcv -- BIOC? +miRNATarget -- http://www.microrna.org/microrna/getDownloads.do? +lqs -- ? +gmmExtra -- R-Forge? +glcoxph -- http://datamining.dongguk.ac.kr/R/glcoxph/src/ +notepad.exe -- probably unsatisfiable +WNdb-3.0.tar.gz -- wordnet.princeton.edu +"mark.exe (>= 6.2) (or mark32.exe andmark64.exe) and rel_32.exe (see README.txt), +mark.exe and rel_32.exe (seeREADME.txt)" -- ^notepad.exe +happy.hbrem -- unknown +hgu133a.db, +hgug4112a.db, +hom.Dm.inp.db, +hom.Hs.inp.db, +hom.Mm.inp.db, +hom.Rn.inp.db, +hom.Sc.inp.db, +hugene10sttranscriptcluster.db, +human.db0, +lumiHumanAll.db, +mirbase.db, +moe430a.db, +mogene10sttranscriptcluster.db, +mouse.db0 -- BIOC +"mSQL-2.0.8 (http://www.Hughes.com.au), mSQL-2.0.8 (http://www.Hughes.com.au) or higher" -- +org.Ag.eg.db, +org.At.tair.db, +org.Bt.eg.db, +org.Ce.eg.db, +org.Cf.eg.db, +org.Dm.eg.db, +org.Dr.eg.db, +org.EcK12.eg.db, +org.EcSakai.eg.db, +org.Gg.eg.db, +org.Hs.eg.db, +org.Hs.ipi.db, +org.Mm.eg.db, +org.Mmu.eg.db, +org.Pf.plasmo.db, +org.Pt.eg.db, +org.Rn.eg.db, +org.Sco.eg.db, +org.Sc.sgd.db, +org.Ss.eg.db, +org.Xl.eg.db -- BIOC +pcaGoPromoter.Hs.hg19, +pcaGoPromoter.Mm.mm9, +pcaGoPromoter.Rn.rn4, +pd.genomewidesnp.5, +pd.genomewidesnp.6, +pd.hg18.60mer.expr, +pd.huex.1.0.st.v2, +pd.hugene.1.0.st.v1, +pd.mapping250k.nsp, +pd.mapping250k.sty, +pd.mapping50k.hind240, +pd.mapping50k.xba240, +rae230a.db, +ragene10sttranscriptcluster.db, +rat.db0, +reactome.db -- BIOC +TxDb.Dmelanogaster.UCSC.dm3.ensGene, +TxDb.Hsapiens.UCSC.hg18.knownGene, +TxDb.Hsapiens.UCSC.hg19.knownGene, +TxDb.Mmusculus.UCSC.mm9.knownGene -- BIOC +targetscan.Hs.eg.db, +targetscan.Mm.eg.db -- BIOC +seqnames.db, +SIFT.Hsapiens.dbSNP132 -- BIOC +SNPlocs.Hsapiens.dbSNP.20100427, +SNPlocs.Hsapiens.dbSNP.20110815, +SNPlocs.Hsapiens.dbSNP.20111119 -- BIOC +RmiR.Hs.miRNA -- BIOC +SciViews-K -- http://www.sciviews.org/SciViews-K +Xba.regions -- ? diff --git a/simple-deprules.d/net b/simple-deprules.d/net new file mode 100644 index 0000000..b739b80 --- /dev/null +++ b/simple-deprules.d/net @@ -0,0 +1,24 @@ +#deptype sys + +net-misc/curl { + curl (version 7.12.0) http://curl.haxx.se + curl (version 7.12.0 or higher) + curl (version 7.12.0 or higher) http://curl.haxx.se + curl (version 7.12.0 or higher) + curl (version 7.14.0 or higher) http://curl.haxx.se + you will often have toexplicitly install libcurl-devel to have the header files andthe libcurl library. + libcurl (version 7.14.0 or higher)http://curl.haxx.se. On Linux systems +} +~net-misc/curl { + curl + libcurl +} + +# FIXME +net-libs/czmq :: libzmq + +net-misc/s3cmd :: s3cmd + +virtual/ssh { + ssh daemon on the server side only:see the rreval manual (vignette) for details. +} diff --git a/simple-deprules.d/nvidia b/simple-deprules.d/nvidia new file mode 100644 index 0000000..a508e1b --- /dev/null +++ b/simple-deprules.d/nvidia @@ -0,0 +1,27 @@ +#deptype sys + +# lowest cuda version in portage is 3.2 +dev-util/nvidia-cuda-toolkit { + NVIDIA CUDA Toolkit (>= release 3.0) + Nvidia CUDAToolkit (>= release 3.0) + Nvidia's CUDA toolkit (>= release 2.3) + NVIDIA CUDA Toolkit 3.1 or above +} + +# FIXME cuda-toolkit or sdk? +dev-util/nvidia-cuda-toolkit { + nvcc (>= release 2.1) + nvcc (>= release 2.1) nVidia GPU (compute number >=1.3) + nvcc (release 2.3) NVIDIA Cuda Compiler driver + nvcc (release 3.0) NVIDIA Cuda Compiler driver + nvcc (release >= 3.1) (NVIDIA Cuda Compilerdriver) + nvcc release 3.1 (NVIDIA Cuda Compiler driver) +} + +>=dev-util/nvidia-cuda-toolkit-4.1 { + Nvidia's CUDA toolkit (release >= 4.1) +} + +>=x11-drivers/nvidia-drivers-270 { + Nvidia CUDA driver (>= 270.xx.xx) +} diff --git a/simple-deprules.d/other b/simple-deprules.d/other deleted file mode 100644 index 8b13789..0000000 --- a/simple-deprules.d/other +++ /dev/null @@ -1 +0,0 @@ - diff --git a/simple-deprules.d/perl b/simple-deprules.d/perl new file mode 100644 index 0000000..c4e460b --- /dev/null +++ b/simple-deprules.d/perl @@ -0,0 +1,12 @@ +#deptype sys + +# lowest perl version in portage: 5.8 (masked) -> 5.12 +~dev-lang/perl :: perl + +dev-perl/OLE-StorageLite :: OLE::Storage_Lite +dev-perl/Parse-RecDescent :: Parse::RecDescent +dev-perl/Spreadsheet-WriteExcel :: Spreadsheet::WriteExcel +dev-perl/Text-CSV_XS :: Text::CSV_XS + +# FIXME: this is very specific, required by WriteXLS from CRAN +virtual/perl-Encode :: Encode diff --git a/simple-deprules.d/sci b/simple-deprules.d/sci new file mode 100644 index 0000000..4728a8d --- /dev/null +++ b/simple-deprules.d/sci @@ -0,0 +1,53 @@ +#deptype sys + +# == geo == +~sci-geosciences/gmt { + libgmt + gmt +} +~sci-geosciences/grass :: grass + +# == math == + +~sci-mathematics/glpk :: glpk + +~sci-mathematics/jags :: jags +sci-mathematics/jags :: jags (see http://mcmc-jags.sourceforge.net) + +# lowest octave version in portage is 3.4 +sci-mathematics/octave { + Octave (>= 3.2.4) and its development files +} + +# lowest version in portage is 2.3.4-r1 +sci-mathematics/pari { + PARI/GP >= 2.3.0 [strongly recommended for logkda()] + PARI/GP >= 2.3.0 [strongly recommended forlogkda()] + pari/gp +} + +sci-mathematics/singular { + Singular (http://www.singular.uni-kl.de) for exactcalculation of the MFR for graphs without splitting edges (onlyfor Unix systems). +} + +~sci-mathematics/yacas :: yacas +sci-mathematics/yacas { + yacas (= 1.0.63) # instructions on home page + yacas (>= 1.0.63) # instructions on home page +} + +# == misc == + +# FIXME: correct? +~sci-misc/netlogo-bin :: NetLogo + +# == physics == + +# lowest sci-physics/root version in portage is 5.32.03 +sci-physics/root { + root_v5.32.01 - See READMEfile for installation instructions. +} + +# == visualization == + +~sci-visualization/ggobi :: ggobi diff --git a/simple-deprules.d/sci-libs b/simple-deprules.d/sci-libs new file mode 100644 index 0000000..1b2b1d7 --- /dev/null +++ b/simple-deprules.d/sci-libs @@ -0,0 +1,73 @@ +#deptype sys + +~sci-libs/armadillo :: armadillo + +~sci-libs/cddlib :: cddlib + +# lowest fftw-3 version in portage is 3.2.2 +>=sci-libs/fftw-3 { + fftw3 + fftw3 (optional) +} +~sci-libs/fftw :: fftw + +sci-libs/gdal { + GDAL library from http://www.gdal.org/download.html + GDAL library from http://www.remotesensing.org/gdal/download.html +} +~sci-libs/gdal :: gdal + +sci-libs/geos { + for building from source: GEOS fromhttp://trac.osgeo.org/geos/ + for building from source: GEOSfrom http://trac.osgeo.org/geos/ +} +~sci-libs/geos :: geos + +sci-libs/gsl { + gsl. Note: users should have GSL installed. Windowsusers: 'consult the README file available in the inst directoryof the source distribution for necessary configurationinstructions'. + gsl (with development libraries) +} +~sci-libs/gsl { + GNU GSL + gsl + libgsl + libgslcblas + GNU GSL for the GSL random-number generators + GNU GSL forthe GSL random-number generators + GNU Scientific Library (GSL) +} + +~sci-libs/hdf5 :: hdf5 + +~sci-libs/itpp { + itpp + libitpp +} + +# FIXME: dev-lang/R[lapack]? +virtual/lapack { + LAPACK sharedlibrary + LAPACKshared library +} + +sci-libs/lapack-atlas :: lapack_atlas + +#FIXME +sci-libs/libsvm :: SVMlight + +~sci-libs/mkl :: Intel MKL + +sci-libs/netcdf :: netcdf library version 4.1 or later +~sci-libs/netcdf :: netcdf + +sci-libs/proj :: proj 4.4.6 or higher (http://proj.maptools.org/) + + +# FIXME, portage version is 2.1.21 +sci-libs/udunits :: udunits (>= 1.11.7) or udunits2(>= 2.1.22) +~sci-libs/udunits { + udunits + udunits-2 +} + +virtual/blas :: blas diff --git a/simple-deprules.d/selfdeps b/simple-deprules.d/selfdeps index d3306ad..7350593 100644 --- a/simple-deprules.d/selfdeps +++ b/simple-deprules.d/selfdeps @@ -1,8 +1,52 @@ -~fftw -~sound -~audio -~rgl -~rpanel -~tuneR -~flac -~tcltk +#deptype pkg + +# FIXME: this may be incorrect +~sci-R/BSgenome { + BSgenome.Celegans.UCSC.ce2 + BSgenome.Dmelanogaster.UCSC.dm3 + BSgenome.Ecoli.NCBI.20080805 + BSgenome.Hsapiens.UCSC.hg18 + BSgenome.Hsapiens.UCSC.hg19 + BSgenome.Mmusculus.UCSC.mm9 + BSgenome.Rnorvegicus.UCSC.rn4 + BSgenome.Scerevisiae.UCSC.sacCer2 +} + +sci-R/chron :: get.hist.quote needs packagechron. + +# FIXME: correct? +~sci-R/CoCo { + CoCoCore + CoCoObjects + CoCoRaw +} + +sci-R/csound { + 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 + playitbyr creates sound using the csound package + which requires the free and open source software synthesizerCsound +} + +~sci-R/mimR :: mim + +sci-R/MVA { + white.test needs packagemva + white.test needs package mva +} + +sci-R/quadprog :: portfolio.optim needs package quadprog + +sci-R/rgl :: rgl packages for rendering + +~sci-R/sgeostat :: geostat. + +sci-R/survival4 :: survival4 if survival models are to be used. +~sci-R/survival5 :: survival5 for some examples +sci-R/survival5 :: survival5 if survival models are to be used. + +~sci-R/VhayuR :: Vhayu + +sci-R/xgobi { + xgobi must be installed additionally + xgobi & xgvis programs: http://www.research.att.com/areas/stat/xgobi/ +} diff --git a/simple-deprules.d/sys b/simple-deprules.d/sys new file mode 100644 index 0000000..3b793d0 --- /dev/null +++ b/simple-deprules.d/sys @@ -0,0 +1,16 @@ +#deptype sys + +~sys-libs/db { + BerkelyDB + BerkeleyDB + Oracle Berkeley DB 11gR2 +} + +~sys-libs/zlib :: zlib +sys-libs/zlib :: zlib (optional) + +# => sys-cluster/ +~virtual/mpi { + LamMPI(>= 6.5.9) or MPICH2(>= 1.0.2) or OpenMPI () + LamMpi(>= 6.5.9) or Mpich2(>= 1.0.2) +} diff --git a/simple-deprules.d/system.set b/simple-deprules.d/system.set new file mode 100644 index 0000000..7ee9fdc --- /dev/null +++ b/simple-deprules.d/system.set @@ -0,0 +1,30 @@ +#deptype sys + +# @system +! { + GNU Make + andg++ GNU compiler (a nvcc-compatible version of g++ is needed + andg++ GNU compiler version 3.4 (version 4.4 is not yet compatiblewith nvcc). + chmod) +} + +% :: gcc +# FIXME: newer gcc versions could work, too += 1.2 http://www.cairographics.org/) +~x11-libs/cairo :: cairo + +~x11-libs/gtk+ :: gtk+ + +~x11-libs/pango :: pango + +x11-libs/qt-core { + qt + Qt4 libraries and headers (http://qt.nokia.com) +} + +x11-misc/xclip { + xclip (Linux) +} + +virtual/opencl { + OpenCL library + OpenCl +} + +~virtual/glu :: GLU Library +virtual/opengl :: opengl