Disable some broken R packages.
This commit is contained in:
Peter Simons
parent
d5017499a2
commit
80101c8329
@ -647,286 +647,289 @@ let
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];
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# Packages which cannot be installed due to lack of dependencies or other reasons.
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brokenPackages = [ # sort -t '#' -k 2
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"V8" # compilation error
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"metabolomics" # depends on broken crmn
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"selectspm" # depends on broken ecespa
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"BLCOP" # depends on broken fPortfolio
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"MXM" # depends on broken gRbase
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"bamboo" # depends on broken jvmr
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"flexCWM" # depends on broken mixture
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"pmcgd" # depends on broken mixture
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"retistruct" # depends on broken RImageJROI
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"ROI_plugin_symphony" # depends on broken Rsymphony
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"ChemoSpec" # depends on broken speaq
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"CARrampsOcl" # depends on OpenCL
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"gmatrix" # depends on proprietary cudatoolkit
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"gputools" # depends on proprietary cudatoolkit
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"iFes" # depends on proprietary cudatoolkit
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"SOD" # depends on proprietary cudatoolkit
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"WideLM" # depends on proprietary cudatoolkit
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"OpenCL" # FIXME: requires CL/opencl.h
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"Rsymphony" # FIXME: requires SYMPHONY
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"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
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"jomo" # linking errors
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"mixture" # mixture.so: undefined symbol: dtrmm_
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"rDEA" # no such file or directory
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"demi" # requires affy, affxparser, and oligo
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"KANT" # requires affy, and Biobase
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"pathClass" # requires affy, and Biobase
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"msarc" # requires AnnotationDbi
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"ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
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brokenPackages = [
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"ACNE" # requires aroma_affymetrix
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"aroma_affymetrix" # requires aroma_core
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"calmate" # requires aroma_core
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"NSA" # requires aroma_core
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"beadarrayFilter" # requires beadarray
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"compendiumdb" # requires Biobase
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"ktspair" # requires Biobase
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"MetaLandSim" # requires Biobase
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"permGPU" # requires Biobase
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"propOverlap" # requires Biobase
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"RobLoxBioC" # requires Biobase
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"RobLox" # requires Biobase
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"IsoGene" # requires Biobase, and affy
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"mGSZ" # requires Biobase, and limma
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"GExMap" # requires Biobase and multtest
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"Statomica" # requires Biobase, multtest
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"netweavers" # requires BiocGenerics, Biobase, and limma
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"NCmisc" # requires BiocInstaller
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"EMDomics" # requires BiocParallel
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"PepPrep" # requires biomaRt
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"snplist" # requires biomaRt
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"ionflows" # requires Biostrings
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"RADami" # requires Biostrings
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"SimRAD" # requires Biostrings, and ShortRead
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"SeqFeatR" # requires Biostrings, qvalue, and widgetTools
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"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
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"FunctionalNetworks" # requires breastCancerVDX, and Biobase
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"js" # requires broken V8
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"minimist" # requires broken V8
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"rJPSGCS" # requires chopsticks
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"clpAPI" # requires clp
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"pcaL1" # requires clp
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"bmrm" # requires clpAPI
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"sequenza" # requires copynumber
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"cplexAPI" # requires CPLEX
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"Rcplex" # requires cplexAPI
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"empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
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"CHAT" # requires DNAcopy
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"ParDNAcopy" # requires DNAcopy
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"PSCBS" # requires DNAcopy
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"dcGOR" # requires dnet
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"gitter" # requires EBImage
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"Rcell" # requires EBImage
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"RockFab" # requires EBImage
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"babel" # requires edgeR
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"edgeRun" # requires edgeR
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"fdrDiscreteNull" # requires edgeR
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"GSAgm" # requires edgeR
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"HTSCluster" # requires edgeR
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"QuasiSeq" # requires edgeR
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"SimSeq" # requires edgeR
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"BcDiag" # requires fabia
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"superbiclust" # requires fabia
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"curvHDR" # requires flowCore
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"RbioRXN" # requires fmcsR, and KEGGREST
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"qdap" # requires gender
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"orQA" # requires genefilter
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"apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light
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"ExomeDepth" # requires GenomicRanges, and Rsamtools
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"rggobi" # requires GGobi
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"miRtest" # requires globaltest, GlobalAncova, and limma
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"PANDA" # requires GO.db
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"BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
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"PubMedWordcloud" # requires GOsummaries
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"eulerian" # requires graph
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"gRapHD" # requires graph
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"msSurv" # requires graph
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"PairViz" # requires graph
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"iRefR" # requires graph, and RBGL
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"pcalg" # requires graph, and RBGL
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"protiq" # requires graph, and RBGL
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"RnavGraph" # requires graph, and RBGL
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"classGraph" # requires graph, and Rgraphviz
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"epoc" # requires graph, and Rgraphviz
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"gridGraphviz" # requires graph, and Rgraphviz
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"QuACN" # requires graph, RBGL
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"D2C" # requires gRbase
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"gRain" # requires gRbase
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"gRc" # requires gRbase
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"gRim" # requires gRbase
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"LogisticDx" # requires gRbase
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"topologyGSA" # requires gRbase
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"gridDebug" # requires gridGraphviz
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"RAM" # requires Heatplus
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"RcppRedis" # requires Hiredis
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"interval" # requires Icens
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"FAMT" # requires impute
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"moduleColor" # requires impute
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"PMA" # requires impute
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"samr" # requires impute
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"swamp" # requires impute
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"WGCNA" # requires impute
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"MetaDE" # requires impute, and Biobase
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"FHtest" # requires interval
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"MSIseq" # requires IRanges
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"SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
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"RefFreeEWAS" # requires isva
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"PhViD" # requires LBE
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"Actigraphy" # SDMTools.so: undefined symbol: X
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"adaptsmoFMRI" # requires spatstat
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"ads" # requires spatstat
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"agridat" # requires pcaMethods
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"aLFQ" # requires protiq
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"AntWeb" # requires leafletR
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"ecoengine" # requires leafletR
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"spocc" # requires leafletR
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"RDieHarder" # requires libdieharder
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"sybilSBML" # requires libSBML
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"CORM" # requires limma
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"DAAGbio" # requires limma
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"DCGL" # requires limma
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"metaMA" # requires limma
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"plmDE" # requires limma
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"SQDA" # requires limma
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"PerfMeas" # requires limma, graph, and RBGL
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"rLindo" # requires LINDO API
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"magma" # requires MAGMA
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"HiPLARM" # requires MAGMA or PLASMA
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"speaq" # requires MassSpecWavelet
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"MAMA" # requires metaMA
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"Rmosek" # requires mosek
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"aoristic" # requires spatstat
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"apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light
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"aroma_affymetrix" # requires aroma_core
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"aroma_cn" # requires PSCBS
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"aroma_core" # requires PSCBS
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"ArrayBin" # requires SAGx
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"babel" # requires edgeR
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"BACA" # requires RDAVIDWebService
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"bamboo" # depends on broken jvmr
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"BcDiag" # requires fabia
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"bdvis" # requres taxize
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"beadarrayFilter" # requires beadarray
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"beadarrayMSV" # requires rggobi
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"bigGP" # requires MPI running. HELP WANTED!
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"doMPI" # requires MPI running. HELP WANTED!
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"metaMix" # requires MPI running. HELP WANTED!
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"pmclust" # requires MPI running. HELP WANTED!
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"MSeasyTkGUI" # requires MSeasyTkGUI
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"hddplot" # requires multtest
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"mutoss" # requires multtest
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"PCS" # requires multtest
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"structSSI" # requires multtest
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"TcGSA" # requires multtest
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"mutossGUI" # requires mutoss
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"Biograph" # requires mvna
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"MSeasy" # requires mzR, and xcms
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"bigpca" # requires NCmisc
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"reader" # requires NCmisc
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"ROracle" # requires OCI
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"Biograph" # requires mvna
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"biotools" # requires rpanel
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"BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
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"BLCOP" # depends on broken fPortfolio
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"bmrm" # requires clpAPI
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"branchLars" # requires Rgraphviz
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"BRugs" # requires OpenBUGS
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"x_ent" # requires opencpu
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"calmate" # requires aroma_core
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"CARrampsOcl" # depends on OpenCL
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"CHAT" # requires DNAcopy
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"ChemoSpec" # depends on broken speaq
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"classGraph" # requires graph, and Rgraphviz
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"clpAPI" # requires clp
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"clusterfly" # requires rggobi
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"compendiumdb" # requires Biobase
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"CORM" # requires limma
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"cplexAPI" # requires CPLEX
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"cqrReg" # requires Rmosek
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"crmn" # requires pcaMethods, and Biobase
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"CrypticIBDcheck" # requires rJPSGCS
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"cudaBayesreg" # requres Rmath
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"curvHDR" # requires flowCore
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"D2C" # requires gRbase
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"DAAGbio" # requires limma
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"dagbag" # requires Rlapack
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"DBKGrad" # requires SDD
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"dbmss" # requires spatstat
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"DCGL" # requires limma
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"dcGOR" # requires dnet
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"demi" # requires affy, affxparser, and oligo
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"DepthProc" # requires samr
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"Digiroo2" # requires spatstat
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"dixon" # requires spatstat
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"dnet" # requires supraHex, graph, Rgraphviz, and Biobase
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"doMPI" # requires MPI running. HELP WANTED!
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"dpcR" # requires spatstat
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"DSpat" # requires spatstat
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"ecespa" # requires spatstat
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"ecoengine" # requires leafletR
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"ecospat" # requires spatstat
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"edgeRun" # requires edgeR
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"EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
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"EMDomics" # requires BiocParallel
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"empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
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"epoc" # requires graph, and Rgraphviz
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"erpR" # requires rpanel
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"ETAS" # requires spatstat
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"eulerian" # requires graph
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"evobiR" # requres taxiz
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"evora" # requires qvalue
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"ExomeDepth" # requires GenomicRanges, and Rsamtools
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"FAMT" # requires impute
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"fdrDiscreteNull" # requires edgeR
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"FHtest" # requires interval
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"flexCWM" # depends on broken mixture
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"fPortfolio" # requires rneos
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"FunctionalNetworks" # requires breastCancerVDX, and Biobase
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"gamlss_demo" # requires rpanel
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"GeneticTools" # requires snpStats
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"GExMap" # requires Biobase and multtest
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"gitter" # requires EBImage
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"gmatrix" # depends on proprietary cudatoolkit
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"GOGANPA" # requires WGCNA
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"gputools" # depends on proprietary cudatoolkit
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"gRain" # requires gRbase
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"gRapHD" # requires graph
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"gRbase" # requires RBGL, and graph
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"gRc" # requires gRbase
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"gridDebug" # requires gridGraphviz
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"gridGraphviz" # requires graph, and Rgraphviz
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"GriegSmith" # requires spatstat
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"gRim" # requires gRbase
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"GSAgm" # requires edgeR
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"GUIDE" # requires rpanel
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"h2o" # tries to download some h2o.jar during its build
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"hasseDiagram" # requires Rgraphviz
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"hddplot" # requires multtest
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"HierO" # requires rneos
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"HiPLARM" # requires MAGMA or PLASMA
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"hpoPlot" # requires Rgraphviz
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"HTSCluster" # requires edgeR
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"iFes" # depends on proprietary cudatoolkit
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"imputeLCMD" # requires pcaMethods, and impute
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"intamapInteractive" # requires spatstat
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"interval" # requires Icens
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"ionflows" # requires Biostrings
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"iRefR" # requires graph, and RBGL
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"IsoGene" # requires Biobase, and affy
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"isva" # requires qvalue
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"jomo" # linking errors
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"js" # requires broken V8
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"jvmr" # tries to download files during its build
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"KANT" # requires affy, and Biobase
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"ktspair" # requires Biobase
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"latticeDensity" # requires spatstat
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"leapp" # requires sva
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"lefse" # SDMTools.so: undefined symbol: X
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"lgcp" # requires rpanel
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"LinRegInteractive" # requires Rpanel
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"LogisticDx" # requires gRbase
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"LOST" # requires pcaMethods
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"ltsk" # requires Rlapack and Rblas
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"magma" # requires MAGMA
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"MAMA" # requires metaMA
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"MEET" # requires pcaMethods, and seqLogo
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"metabolomics" # depends on broken crmn
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"MetaDE" # requires impute, and Biobase
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"MetaLandSim" # requires Biobase
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"metaMA" # requires limma
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"metaMix" # requires MPI running. HELP WANTED!
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"mGSZ" # requires Biobase, and limma
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"MigClim" # SDMTools.So: Undefined Symbol: X
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"minimist" # requires broken V8
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"miRtest" # requires globaltest, GlobalAncova, and limma
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"mixture" # mixture.so: undefined symbol: dtrmm_
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"moduleColor" # requires impute
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"msarc" # requires AnnotationDbi
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"MSeasy" # requires mzR, and xcms
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"MSeasyTkGUI" # requires MSeasyTkGUI
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"MSIseq" # requires IRanges
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"msSurv" # requires graph
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"multiDimBio" # requires pcaMethods
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"mutossGUI" # requires mutoss
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"mutoss" # requires multtest
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"MXM" # depends on broken gRbase
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"NBPSeq" # requires qvalue
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"NCmisc" # requires BiocInstaller
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"netClass" # requires samr
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"nettools" # requires WGCNA
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"netweavers" # requires BiocGenerics, Biobase, and limma
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"NLPutils" # requires qdap
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"NSA" # requires aroma_core
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"OpenCL" # FIXME: requires CL/opencl.h
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"optBiomarker" # requires rpanel
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"ora" # requires ROracle
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"orQA" # requires genefilter
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"PairViz" # requires graph
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"PANDA" # requires GO.db
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"ParDNAcopy" # requires DNAcopy
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"pathClass" # requires affy, and Biobase
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"PatternClass" # SDMTools.So: Undefined Symbol: X
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"pbdBASE" # requires pbdMPI
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"pbdDEMO" # requires pbdMPI
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"pbdDMAT" # requires pbdMPI
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"pbdSLAP" # requires pbdMPI
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"qtlnet" # requires pcalg
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"agridat" # requires pcaMethods
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"LOST" # requires pcaMethods
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"multiDimBio" # requires pcaMethods
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"crmn" # requires pcaMethods, and Biobase
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"imputeLCMD" # requires pcaMethods, and impute
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"MEET" # requires pcaMethods, and seqLogo
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"saps" # requires piano, and survcomp
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"smart" # requires PMA
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"surveillance" # requires polyCub
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"aLFQ" # requires protiq
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"aroma_cn" # requires PSCBS
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"aroma_core" # requires PSCBS
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"NLPutils" # requires qdap
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"RQuantLib" # requires QuantLib
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"evora" # requires qvalue
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"isva" # requires qvalue
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"NBPSeq" # requires qvalue
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"pi0" # requires qvalue
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"RSNPset" # requires qvalue
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"gRbase" # requires RBGL, and graph
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"RSeed" # requires RBGL, and graph
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"BACA" # requires RDAVIDWebService
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"beadarrayMSV" # requires rggobi
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"clusterfly" # requires rggobi
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"PKgraph" # requires rggobi
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"SeqGrapheR" # requires rggobi
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"branchLars" # requires Rgraphviz
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"hasseDiagram" # requires Rgraphviz
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"hpoPlot" # requires Rgraphviz
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"strum" # requires Rgraphviz
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"CrypticIBDcheck" # requires rJPSGCS
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"dagbag" # requires Rlapack
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"ltsk" # requires Rlapack and Rblas
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"cqrReg" # requires Rmosek
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"REBayes" # requires Rmosek
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"fPortfolio" # requires rneos
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"HierO" # requires rneos
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"ora" # requires ROracle
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"biotools" # requires rpanel
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"erpR" # requires rpanel
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"gamlss_demo" # requires rpanel
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"GUIDE" # requires rpanel
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"lgcp" # requires rpanel
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"optBiomarker" # requires rpanel
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"SDD" # requires rpanel
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"soilphysics" # requires rpanel
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"vows" # requires rpanel
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"LinRegInteractive" # requires Rpanel
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"RVideoPoker" # requires Rpanel
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"semiArtificial" # requires RSNNS
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"pcaL1" # requires clp
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"pcalg" # requires graph, and RBGL
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"PCGSE" # requires safe
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"ArrayBin" # requires SAGx
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"DepthProc" # requires samr
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"netClass" # requires samr
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"RSAP" # requires SAPNWRFCSDK
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"DBKGrad" # requires SDD
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"RcmdrPlugin_seeg" # requires seeg
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"EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
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"GeneticTools" # requires snpStats
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"snpEnrichment" # requires snpStats
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"snpStatsWriter" # requires snpStats
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"wgsea" # requires snpStats
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"rysgran" # requires soiltexture
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"adaptsmoFMRI" # requires spatstat
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"ads" # requires spatstat
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"aoristic" # requires spatstat
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"dbmss" # requires spatstat
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"Digiroo2" # requires spatstat
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"dixon" # requires spatstat
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"dpcR" # requires spatstat
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"DSpat" # requires spatstat
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"ecespa" # requires spatstat
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"ecospat" # requires spatstat
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"ETAS" # requires spatstat
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"GriegSmith" # requires spatstat
|
||||
"intamapInteractive" # requires spatstat
|
||||
"latticeDensity" # requires spatstat
|
||||
"PCS" # requires multtest
|
||||
"PepPrep" # requires biomaRt
|
||||
"PerfMeas" # requires limma, graph, and RBGL
|
||||
"permGPU" # requires Biobase
|
||||
"PhViD" # requires LBE
|
||||
"pi0" # requires qvalue
|
||||
"PKgraph" # requires rggobi
|
||||
"plmDE" # requires limma
|
||||
"plsRcox" # requires survcomp
|
||||
"PMA" # requires impute
|
||||
"pmcgd" # depends on broken mixture
|
||||
"pmclust" # requires MPI running. HELP WANTED!
|
||||
"polyCub" # requires spatstat
|
||||
"ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
|
||||
"propOverlap" # requires Biobase
|
||||
"protiq" # requires graph, and RBGL
|
||||
"PSCBS" # requires DNAcopy
|
||||
"pubmed_mineR" # requires SSOAP
|
||||
"PubMedWordcloud" # requires GOsummaries
|
||||
"qdap" # requires gender
|
||||
"qtlnet" # requires pcalg
|
||||
"qtpaint" # can't find QtCore libraries
|
||||
"QuACN" # requires graph, RBGL
|
||||
"QuasiSeq" # requires edgeR
|
||||
"RADami" # requires Biostrings
|
||||
"raincpc" # SDMTools.so: undefined symbol: X
|
||||
"rainfreq" # SDMTools.so: undefined symbol: X
|
||||
"RAM" # requires Heatplus
|
||||
"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
|
||||
"RbioRXN" # requires fmcsR, and KEGGREST
|
||||
"Rcell" # requires EBImage
|
||||
"RcmdrPlugin_seeg" # requires seeg
|
||||
"Rcplex" # requires cplexAPI
|
||||
"RcppRedis" # requires Hiredis
|
||||
"rDEA" # no such file or directory
|
||||
"RDieHarder" # requires libdieharder
|
||||
"reader" # requires NCmisc
|
||||
"REBayes" # requires Rmosek
|
||||
"RefFreeEWAS" # requires isva
|
||||
"retistruct" # depends on broken RImageJROI
|
||||
"rggobi" # requires GGobi
|
||||
"RImageJROI" # requires spatstat
|
||||
"rJPSGCS" # requires chopsticks
|
||||
"rLindo" # requires LINDO API
|
||||
"Rmosek" # requires mosek
|
||||
"RnavGraph" # requires graph, and RBGL
|
||||
"rneos" # requires XMLRPC
|
||||
"RNeXML" # requres taxize
|
||||
"RobLoxBioC" # requires Biobase
|
||||
"RobLox" # requires Biobase
|
||||
"RockFab" # requires EBImage
|
||||
"ROI_plugin_symphony" # depends on broken Rsymphony
|
||||
"ROracle" # requires OCI
|
||||
"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
|
||||
"RQuantLib" # requires QuantLib
|
||||
"RSAP" # requires SAPNWRFCSDK
|
||||
"RSeed" # requires RBGL, and graph
|
||||
"rsig" # requires survcomp
|
||||
"RSNPset" # requires qvalue
|
||||
"rsprng" # requres sprng
|
||||
"Rsymphony" # FIXME: requires SYMPHONY
|
||||
"RVideoPoker" # requires Rpanel
|
||||
"rysgran" # requires soiltexture
|
||||
"samr" # requires impute
|
||||
"saps" # requires piano, and survcomp
|
||||
"SDD" # requires rpanel
|
||||
"seeg" # requires spatstat
|
||||
"selectspm" # depends on broken ecespa
|
||||
"semiArtificial" # requires RSNNS
|
||||
"SeqFeatR" # requires Biostrings, qvalue, and widgetTools
|
||||
"SeqGrapheR" # requires rggobi
|
||||
"sequenza" # requires copynumber
|
||||
"SGCS" # requires spatstat
|
||||
"siar" # requires spatstat
|
||||
"SimRAD" # requires Biostrings, and ShortRead
|
||||
"SimSeq" # requires edgeR
|
||||
"siplab" # requires spatstat
|
||||
"smart" # requires PMA
|
||||
"snpEnrichment" # requires snpStats
|
||||
"snplist" # requires biomaRt
|
||||
"snpStatsWriter" # requires snpStats
|
||||
"SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
|
||||
"SOD" # depends on proprietary cudatoolkit
|
||||
"soilphysics" # requires rpanel
|
||||
"sparr" # requires spatstat
|
||||
"spatialsegregation" # requires spatstat
|
||||
"SpatialVx" # requires spatstat
|
||||
"speaq" # requires MassSpecWavelet
|
||||
"spocc" # requires leafletR
|
||||
"SQDA" # requires limma
|
||||
"Statomica" # requires Biobase, multtest
|
||||
"StochKit2R" # tarball is invalid on server
|
||||
"stpp" # requires spatstat
|
||||
"trip" # requires spatstat
|
||||
"pubmed_mineR" # requires SSOAP
|
||||
"dnet" # requires supraHex, graph, Rgraphviz, and Biobase
|
||||
"plsRcox" # requires survcomp
|
||||
"rsig" # requires survcomp
|
||||
"leapp" # requires sva
|
||||
"ttScreening" # requires sva, and limma
|
||||
"GOGANPA" # requires WGCNA
|
||||
"nettools" # requires WGCNA
|
||||
"rneos" # requires XMLRPC
|
||||
"structSSI" # requires multtest
|
||||
"strum" # requires Rgraphviz
|
||||
"superbiclust" # requires fabia
|
||||
"surveillance" # requires polyCub
|
||||
"swamp" # requires impute
|
||||
"sybilSBML" # requires libSBML
|
||||
"taxize" # requres bold
|
||||
"cudaBayesreg" # requres Rmath
|
||||
"rsprng" # requres sprng
|
||||
"evobiR" # requres taxiz
|
||||
"bdvis" # requres taxize
|
||||
"RNeXML" # requres taxize
|
||||
"TcGSA" # requires multtest
|
||||
"topologyGSA" # requires gRbase
|
||||
"TR8" # requres taxize
|
||||
"Actigraphy" # SDMTools.so: undefined symbol: X
|
||||
"lefse" # SDMTools.so: undefined symbol: X
|
||||
"raincpc" # SDMTools.so: undefined symbol: X
|
||||
"rainfreq" # SDMTools.so: undefined symbol: X
|
||||
"MigClim" # SDMTools.So: Undefined Symbol: X
|
||||
"PatternClass" # SDMTools.So: Undefined Symbol: X
|
||||
"jvmr" # tries to download files during its build
|
||||
"h2o" # tries to download some h2o.jar during its build
|
||||
"trip" # requires spatstat
|
||||
"ttScreening" # requires sva, and limma
|
||||
"V8" # compilation error
|
||||
"vows" # requires rpanel
|
||||
"WGCNA" # requires impute
|
||||
"wgsea" # requires snpStats
|
||||
"WideLM" # depends on proprietary cudatoolkit
|
||||
"x_ent" # requires opencpu
|
||||
"zoib" # tarball is invalid on server
|
||||
];
|
||||
|
||||
otherOverrides = old: new: {
|
||||
|
||||
Loading…
Reference in New Issue
Block a user