#! 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# this file is out of date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 -- ?