From d015768fc975f3abfac9ce91d5c0ff3c1c30ca79 Mon Sep 17 00:00:00 2001 From: André Erdmann Date: Tue, 27 Aug 2013 18:05:48 +0200 Subject: move config/simple-deprules.d/missing{,.old} --- config/simple-deprules.d/missing | 265 ----------------------------------- config/simple-deprules.d/missing.old | 265 +++++++++++++++++++++++++++++++++++ 2 files changed, 265 insertions(+), 265 deletions(-) delete mode 100644 config/simple-deprules.d/missing create mode 100644 config/simple-deprules.d/missing.old (limited to 'config') diff --git a/config/simple-deprules.d/missing b/config/simple-deprules.d/missing deleted file mode 100644 index ad66be2..0000000 --- a/config/simple-deprules.d/missing +++ /dev/null @@ -1,265 +0,0 @@ -#! NOPARSE - -# this file is out of date - -# === missing === -ALL -ALLMLL -ActiveTcl -AffymetrixDataTestFiles -- BIOC experimental -AmpAffyExample -- BIOC experimental -ArcGIS -- seems to be some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.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/config/simple-deprules.d/missing.old b/config/simple-deprules.d/missing.old new file mode 100644 index 0000000..ad66be2 --- /dev/null +++ b/config/simple-deprules.d/missing.old @@ -0,0 +1,265 @@ +#! NOPARSE + +# this file is out of date + +# === 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.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 -- ? -- cgit v1.2.3-65-gdbad