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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oneChannelGUI_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/oneChannelGUI.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oneChannelGUI/DESCRIPTION’ ... OK
* this is package ‘oneChannelGUI’ version ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘Biobase’ ‘affylmGUI’ ‘tkrplot’ ‘tkWidgets’ ‘IRanges’ ‘Rsamtools’
‘Biostrings’ ‘siggenes’ ‘chimera’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oneChannelGUI’ can be installed ... [55s/60s] OK
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
vignettes 5.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘affy’ ‘AffyCompatible’ ‘affyPLM’ ‘annaffy’ ‘annotate’ ‘baySeq’
‘biomaRt’ ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’
‘BSgenome.Mmusculus.UCSC.mm9’ ‘BSgenome.Rnorvegicus.UCSC.rn4’
‘ChIPpeakAnno’ ‘chipseq’ ‘cummeRbund’ ‘DESeq’ ‘DEXSeq’ ‘EDASeq’
‘edgeR’ ‘genefilter’ ‘GenomeGraphs’ ‘Genominator’ ‘goseq’ ‘GOstats’
‘HuExExonProbesetLocation’ ‘limma’ ‘maSigPro’ ‘MergeMaid’ ‘metaArray’
‘MoExExonProbesetLocation’ ‘multtest’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’
‘org.Rn.eg.db’ ‘pamr’ ‘pdmclass’ ‘preprocessCore’ ‘R.utils’
‘RaExExonProbesetLocation’ ‘RankProd’ ‘Rgraphviz’ ‘RmiR’
‘RmiR.Hs.miRNA’ ‘rtracklayer’ ‘sizepower’ ‘snow’ ‘ssize’ ‘stats’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.consistentFilter: warning in get("midas.p.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
.consistentFilter: warning in get("AltSplRP.e.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
.consistentFilter: warning in get("AltSplRP.e.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
.consistentFilter: warning in get("midas.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
.consistentFilter: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
.consistentFilter: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
.consistentFilter: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
.consistentFilter: warning in get("consistentP", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
.mappingWgenominator: warning in get("NGSprimaryMapping.Available", env
= affylmGUIenvironment): partial argument match of 'env' to 'envir'
.mappingWgenominator: warning in get("NGSprimaryMapping", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
AptMidas: warning in get("NormalizedAffyData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
AptMidas: warning in get("exonAffyData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
AptMidas: warning in get("libDir.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
AptMidas: warning in get("whichLib", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
AptMidas: warning in get("libDir", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
AptMidas: warning in get("aptDir.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
AptMidas: warning in get("aptDir", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
AptMidas: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
AptMidas: warning in get("exonAffyData", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
bayseqInterface: warning in get("SOCKSnum", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
bayseqInterface: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
bayseqInterface: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
bayseqInterface: warning in get("Iterations", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
bowtieDownload: warning in writeXStringSet(hsfa, file = "ncHs.fa"):
partial argument match of 'file' to 'filepath'
bowtieDownload: warning in writeXStringSet(mmfa, file = "ncMm.fa"):
partial argument match of 'file' to 'filepath'
bowtieDownload: warning in writeXStringSet(rnfa, file = "ncRn.fa"):
partial argument match of 'file' to 'filepath'
bowtieDownload: warning in writeXStringSet(bofa, file = "ncBo.fa"):
partial argument match of 'file' to 'filepath'
buildingLocalAnnotation: warning in get("UserNameText", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
buildingLocalAnnotation: warning in get("UserPwText", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
cdsDiff: warning in get("Targets", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
combineGeoMSF: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
combineGeoMSF: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
consistentFilters: warning in get("midas.p.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
consistentFilters: warning in get("AltSplRP.e.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
consistentFilters: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
consistentFilters: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
consistentFilters: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
consistentFilters: warning in get("midas.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
consistentFilters: warning in get("AltSplRP.e.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
consistentFilters: warning in get("consistentP", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
consistentFilters: warning in get("spliceIndexData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
cosieWrapper: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
cosieWrapper: warning in get("whichLib", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
cosieWrapper: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
createDir: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
cuffdiff: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
cuffdiff: warning in get("Cores", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
cufflinks: warning in get("Cores", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
cuffmerge: warning in get("Cores", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
dabgFilter: warning in get("dabg.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
dabgFilter: warning in get("exonAffyData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
dabgFilter: warning in get("exonAffyData", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
DESeqInterface: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
DESeqInterface: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
EDAbetweenLane: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
EDAbetweenLane: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
EDAbetweenLane: warning in assign("NormalizedAffyData",
NormalizedAffyData, env = affylmGUIenvironment): partial argument
match of 'env' to 'envir'
EDAbiasPlot: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
EDAbiasPlot: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
EDAboxplot: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
EDAboxplot: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
EDANtFreq: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
EDANtFreq: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
EDAplotQuality: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
EDAplotQuality: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
EDAreadNumber: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
EDAreadNumber: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
EDAwithinLane: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
EDAwithinLane: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
EDAwithinLane: warning in assign("NormalizedAffyData",
NormalizedAffyData, env = affylmGUIenvironment): partial argument
match of 'env' to 'envir'
edgerInterface: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
edgerInterface: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
edgerInterface: warning in get("NGSscaling.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
edgerInterface: warning in get("NGSscaling", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
edgeRNorm: warning in get("NGSscaling.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
edgeRNorm: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
edgeRNorm: warning in get("mappedReads", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
edgeRNorm: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
edgeRNorm: warning in assign("NGSscaling.Available", TRUE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
edgeRNorm: warning in assign("NGSscaling", scaledReads, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSpl: warning in get("spliceIndexData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSpl: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSpl: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSplFilter: warning in get("spliceIndexData.Available", env
= affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSplFilter: warning in get("AltSplRP.e.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSplFilter: warning in get("AltSplRP.e.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSplFilter: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSplFilter: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSplFilter: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
erankProdAltSplFilter: warning in get("AltSplRPnum", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonContrasts: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonsSpecific2as: warning in get("mapping2ensembl.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonsSpecific2as: warning in get("mapping2ensembl", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonTopTableExtract: warning in get("AltSplLimma.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonTopTableExtract: warning in get("spliceIndexData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonTopTableExtract: warning in get("AltSplLimma", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonTopTableExtract: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonTopTableExtract: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonTopTableExtract: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exonTopTableExtract: warning in get("Midasnum", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
exportFASTA: warning in writeXStringSet(hsfa, file = "ncHs.fa"):
partial argument match of 'file' to 'filepath'
exportFASTA: warning in writeXStringSet(mmfa, file = "ncMm.fa"):
partial argument match of 'file' to 'filepath'
exportFASTA: warning in writeXStringSet(rnfa, file = "ncRn.fa"):
partial argument match of 'file' to 'filepath'
exportFASTA: warning in writeXStringSet(bofa, file = "ncBo.fa"):
partial argument match of 'file' to 'filepath'
filteringmiRtargets: warning in get("miRname", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
filteringmiRtargets: warning in get("whichArrayPlatform", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
geneDiff: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
genomePlot: warning in get("exonAffyData", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
goseqInterface: warning in get("Targets", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
goseqInterface: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in
get("spliceIndexData.Available", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("Targets", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("exprConsoleLibs", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("midas.p.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("AltSplRP.e.Available", env
= affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("AltSplLimma.Available",
env = affylmGUIenvironment): partial argument match of 'env' to
'envir'
inspecting.one.splice.index: warning in get("ProbesetNameText", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("midas.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("AltSplLimma", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.one.splice.index: warning in get("AltSplRP.e.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("spliceIndexData.Available",
env = affylmGUIenvironment): partial argument match of 'env' to
'envir'
inspecting.splice.index: warning in get("midas.p.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("AltSplRP.e.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("AltSplLimma.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("Targets", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("exprConsoleLibs", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("midas.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("AltSplLimma", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in get("AltSplRP.e.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
inspecting.splice.index: warning in assign("detected.splicing",
selected.altsplg, env = affylmGUIenvironment): partial argument match
of 'env' to 'envir'
intensityFilter: warning in get("intronicBg", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
intronicBg: warning in get("intronicBg", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
IPAlistFilter: warning in get("NormalizedAffyData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
IPAlistFilter: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
IPAlistFilter: warning in read.table(tempFileName, sep = "\t", header =
F, as.is = TRUE, na.string = "", quote = ""): partial argument match
of 'na.string' to 'na.strings'
IPAlistFilter: warning in assign("NormalizedAffyData", x, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
iqrFilter: warning in get("whichArrayPlatform", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
isoDiff: warning in get("Targets", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
largedatasetNorm: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
largedatasetNorm: warning in assign("NormalizedAffyData",
NormalizedAffyData, env = affylmGUIenvironment): partial argument
match of 'env' to 'envir'
limma2paired: warning in mget(featureNames(NormalizedAffyData), env =
getDataEnv("ORF", annLib), ifnotfound = NA): partial argument match
of 'env' to 'envir'
limma2paired: warning in mget(featureNames(NormalizedAffyData), env =
getDataEnv("GENENAME", annLib), ifnotfound = NA): partial argument
match of 'env' to 'envir'
limmaExons: warning in get("exonAffyData", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
listFilter: warning in get("whichArrayPlatform", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
log2Conversion: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
log2Conversion: warning in assign("NormalizedAffyData",
NormalizedAffyData, env = affylmGUIenvironment): partial argument
match of 'env' to 'envir'
log2Conversion: warning in assign("NGSconversion.available", TRUE, env
= affylmGUIenvironment): partial argument match of 'env' to 'envir'
mapping2ensembl: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
mapping2ensembl: warning in get("spliceIndexData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
mapping2ensembl: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
mapping2ensembl: warning in get("midas.p.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
mapping2ensembl: warning in get("midas.p", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
mapping2ensembl: warning in get("AltSplRP.e.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
mapping2ensembl: warning in get("AltSplRP.e.p", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
midasFilter: warning in get("midas.p.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
midasFilter: warning in get("spliceIndexData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
midasFilter: warning in get("midas.p", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
midasFilter: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
midasFilter: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
midasFilter: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
midasFilter: warning in get("Midasnum", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
ML.edesign: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
mRNAbowtieRun: warning in get("Threads", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
NewLimmaFile: warning in assign("geoPlatform", tt, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
NewLimmaFile: warning in assign("trainAffyData.available", FALSE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
NewLimmaFile: warning in assign("testAffyData.available", FALSE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
NewLimmaFileNGS: warning in assign("geoPlatform", tt, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
NewLimmaFileNGS: warning in assign("trainAffyData.available", FALSE,
env = affylmGUIenvironment): partial argument match of 'env' to
'envir'
NewLimmaFileNGS: warning in assign("testAffyData.available", FALSE, env
= affylmGUIenvironment): partial argument match of 'env' to 'envir'
NewLimmaFileNGS: warning in assign("NGS.Available", FALSE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
NewLimmaFileNGS: warning in assign("NGSconversion.available", FALSE,
env = affylmGUIenvironment): partial argument match of 'env' to
'envir'
NewLimmaFileNGS: warning in assign("NGSprimaryMapping.Available", TRUE,
env = affylmGUIenvironment): partial argument match of 'env' to
'envir'
oneChannelGUI: warning in assign("geoPlatform", tt, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
oneChannelGUI: warning in assign("trainAffyData.available", FALSE, env
= affylmGUIenvironment): partial argument match of 'env' to 'envir'
oneChannelGUI: warning in assign("testAffyData.available", FALSE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
oneChannelGUI: warning in assign("NGS.Available", FALSE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
oneChannelGUI: warning in assign("NGSconversion.available", FALSE, env
= affylmGUIenvironment): partial argument match of 'env' to 'envir'
oneChannelGUI: warning in assign("Genominator.Available", FALSE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
oneChannelGUI: warning in assign("NGSscaling.Available", FALSE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
oneChannelGUI: warning in assign("NGSprimaryMapping.Available", FALSE,
env = affylmGUIenvironment): partial argument match of 'env' to
'envir'
OpenAGeoFile: warning in assign("geoPlatform", geoPlatform, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
OpenBeadStudioFiles: warning in assign("illuData", illuData, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
OpenBeadStudioFiles: warning in assign("illuData.Available", TRUE, env
= affylmGUIenvironment): partial argument match of 'env' to 'envir'
OpenBeadStudioFiles: warning in assign("NormalizedAffyData",
NormalizedAffyData, env = affylmGUIenvironment): partial argument
match of 'env' to 'envir'
OpenBeadStudioFiles: warning in assign("NormalizedAffyData.Available",
TRUE, env = affylmGUIenvironment): partial argument match of 'env' to
'envir'
OpenGeoFiles: warning in get("geoPlatform", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
plierToZero: warning in get("NormalizedAffyData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
plierToZero: warning in get("exonAffyData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
plierToZero: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
plierToZero: warning in assign("NormalizedAffyData",
NormalizedAffyData, env = affylmGUIenvironment): partial argument
match of 'env' to 'envir'
plierToZero: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
plierToZero: warning in assign("exonAffyData", exonAffyData, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
qcMDS: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
qcMDS: warning in get("mappedReads", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
qcMDS: warning in get("Targets", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
qcMDS: warning in get("NGSscaling.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
qcMDS: warning in get("NGSscaling", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
rankingConversion: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
rankingConversion: warning in assign("NormalizedAffyData",
NormalizedAffyData, env = affylmGUIenvironment): partial argument
match of 'env' to 'envir'
rankProd: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
rankProd: warning in mget(featureNames(NormalizedAffyData), env =
getDataEnv("ORF", annLib), ifnotfound = NA): partial argument match
of 'env' to 'envir'
rankProd: warning in mget(featureNames(NormalizedAffyData), env =
getDataEnv("GENENAME", annLib), ifnotfound = NA): partial argument
match of 'env' to 'envir'
refiningPeaks: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
refiningPeaks: warning in get("chrsLength", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
refiningPeaks: warning in get("mergingThr", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
retrieveMirTargets: warning in get("miRname", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
retrievePSRseq1gid: warning in get("exprConsoleLibs", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
reviqrFilter: warning in get("whichArrayPlatform", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
sample.size.evaluation: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
sample.size.evaluation: warning in get("FCnum", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
sample.size.evaluation: warning in get("Powernum", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
sample.size.evaluation: warning in get("SLnum", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
sample.size.evaluation1: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
showTopTable: warning in mget(featureNames(NormalizedAffyData), env =
getDataEnv("ORF", annLib), ifnotfound = NA): partial argument match
of 'env' to 'envir'
showTopTable: warning in mget(featureNames(NormalizedAffyData), env =
getDataEnv("GENENAME", annLib), ifnotfound = NA): partial argument
match of 'env' to 'envir'
siggenes: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
simFilter: warning in get("spliceIndexData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
simFilter: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
spliceIndex: warning in get("exprConsoleLibs", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
spliceIndex: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
spliceIndex: warning in get("exonAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
tophat: warning in get("MateInnerDist", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
tophat: warning in get("Cores", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
tophat: warning in write.table(df.config, file =
paste("tophat_config_", tmp, ".txt", sep = ""), sep = "\t", quote =
F, row.name = F, col.name = F): partial argument match of 'row.name'
to 'row.names'
tophat: warning in write.table(df.config, file =
paste("tophat_config_", tmp, ".txt", sep = ""), sep = "\t", quote =
F, row.name = F, col.name = F): partial argument match of 'col.name'
to 'col.names'
tophatrun: warning in get("Cores", env = affylmGUIenvironment): partial
argument match of 'env' to 'envir'
trainTest: warning in get("NormalizedAffyData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
trainTest: warning in assign("trainAffyData", trainAffyData, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
trainTest: warning in assign("trainAffyData.available", TRUE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
trainTest: warning in assign("testAffyData", testAffyData, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
trainTest: warning in assign("testAffyData.available", TRUE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
trainTest: warning in assign("testAffyData.available", FALSE, env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
trainTest: warning in get("trainAffyData", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
trainTest: warning in get("Permutations", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
trainTest: warning in get("PSsize", env = affylmGUIenvironment):
partial argument match of 'env' to 'envir'
variantSI: warning in get("spliceIndexData.Available", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
variantSI: warning in get("spliceIndexData", env =
affylmGUIenvironment): partial argument match of 'env' to 'envir'
VennDiagram: warning in mget(mySel[, 1], env = getDataEnv("ENTREZID",
lib), ifnotfound = NA): partial argument match of 'env' to 'envir'
.aptDir: no visible binding for global variable ‘.affylmGUIglobals’
.consistentFilter: no visible binding for global variable
‘.affylmGUIglobals’
.consistentFilter: no visible binding for global variable
‘affylmGUIenvironment’
.consistentFilter : onOK: no visible binding for global variable
‘affylmGUIenvironment’
.consistentFilter : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
.downloadLibs: no visible binding for global variable
‘.affylmGUIglobals’
.downloadLibs: no visible binding for global variable
‘affylmGUIenvironment’
.exonTopTable: no visible binding for global variable
‘affylmGUIenvironment’
.exonTopTable: no visible global function definition for ‘eBayes’
.fromNGStoDf: no visible binding for global variable ‘tmpIR’
.GetContrasts: no visible binding for global variable
‘affylmGUIenvironment’
.GetContrasts: no visible global function definition for ‘limmaExon’
.gettingEG: no visible binding for global variable
‘affylmGUIenvironment’
.gettingEG: no visible binding for global variable ‘huex.annotation’
.gettingEG: no visible binding for global variable ‘moex.annotation’
.gettingEG: no visible binding for global variable ‘raex.annotation’
.gettingEG: no visible global function definition for ‘lookUp’
.gettingOneEG: no visible binding for global variable
‘.affylmGUIglobals’
.gettingOneEG: no visible binding for global variable
‘affylmGUIenvironment’
.gettingOneEG: no visible binding for global variable ‘huex.annotation’
.gettingOneEG: no visible global function definition for ‘lookUp’
.gettingOneEG: no visible binding for global variable ‘moex.annotation’
.gettingOneEG: no visible binding for global variable ‘raex.annotation’
.mappingWgenominator: no visible binding for global variable
‘affylmGUIenvironment’
.mappingWgenominator: no visible global function definition for
‘aggregateExpData’
.mappingWgenominator: no visible global function definition for
‘importToExpData’
.mappingWgenominator: no visible global function definition for
‘summarizeByAnnotation’
.pamr.confusion.mod: no visible binding for global variable
‘which.is.max’
.peaksDetector: no visible global function definition for ‘extendReads’
.perm.pamr: no visible global function definition for ‘pamr.train’
.perm.pdmclass: no visible global function definition for ‘pdmClass’
.perm.pdmclass: no visible global function definition for ‘pdmClass.cv’
.perm.pdmclass: no visible global function definition for ‘confusion’
.rawpCheckExons: no visible binding for global variable
‘affylmGUIenvironment’
.rawpCheckExons: no visible binding for global variable
‘.affylmGUIglobals’
.resize: no visible binding for global variable ‘.affylmGUIglobals’
.resize: no visible binding for global variable ‘affylmGUIenvironment’
.resize : onOK: no visible binding for global variable
‘affylmGUIenvironment’
.resize : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
.resize: no visible global function definition for
‘makeRectangleOverlay’
.resize: no visible global function definition for ‘DisplayPars’
.resize: no visible global function definition for ‘gdPlot’
.unionReads: no visible global function definition for ‘GenomeData’
.unionReads: no visible global function definition for ‘gdapply’
adaptorTrimm: no visible binding for global variable
‘affylmGUIenvironment’
adaptorTrimm : onOK: no visible binding for global variable
‘affylmGUIenvironment’
addAnnLib: no visible binding for global variable
‘affylmGUIenvironment’
addAnnLib: no visible binding for global variable ‘.affylmGUIglobals’
addAnnLib : onOK: no visible binding for global variable
‘affylmGUIenvironment’
addAnnLib : onOK: no visible binding for global variable
‘.affylmGUIglobals’
addAnnLib : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
addga: no visible binding for global variable ‘.affylmGUIglobals’
affyPlotMA: no visible binding for global variable
‘affylmGUIenvironment’
affyPlotMA: no visible binding for global variable ‘.affylmGUIglobals’
affyPlotMA : plotFunction: no visible binding for global variable
‘.affylmGUIglobals’
annotateNGSeset: no visible binding for global variable
‘.affylmGUIglobals’
annotateNGSeset: no visible binding for global variable
‘affylmGUIenvironment’
annotateNGSeset: no visible global function definition for
‘annotatePeakInBatch’
aptFolder: no visible binding for global variable ‘.affylmGUIglobals’
aptFolder: no visible binding for global variable
‘affylmGUIenvironment’
AptMidas: no visible binding for global variable ‘affylmGUIenvironment’
AptMidas: no visible binding for global variable ‘.affylmGUIglobals’
AptMidas: no visible binding for global variable ‘tmp’
AptMidas: no visible binding for global variable ‘tt’
bayseqInterface: no visible binding for global variable
‘.affylmGUIglobals’
bayseqInterface : onOK: no visible binding for global variable
‘affylmGUIenvironment’
bayseqInterface : onOK: no visible binding for global variable
‘.affylmGUIglobals’
bayseqInterface : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
bayseqInterface: no visible binding for global variable
‘affylmGUIenvironment’
bayseqInterface: no visible global function definition for
‘getPriors.NB’
bayseqInterface: no visible global function definition for
‘getLikelihoods.NB’
bayseqInterface: no visible global function definition for ‘topCounts’
bayseqInterface : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
bayseqInterface : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
bayseqInterface : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
bayseqInterface: no visible binding for global variable ‘ReturnVal’
biomartFilter: no visible binding for global variable
‘.affylmGUIglobals’
biomartFilter: no visible global function definition for ‘useMart’
biomartFilter: no visible global function definition for ‘useDataset’
biomartFilter: no visible global function definition for ‘getBM’
bowtieBuilt: no visible binding for global variable ‘.affylmGUIglobals’
bowtieBuilt : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
bowtieBuilt : onOK: no visible binding for global variable
‘.affylmGUIglobals’
bowtieBuilt : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
bowtieBuilt: no visible binding for global variable
‘affylmGUIenvironment’
bowtieDownload: no visible binding for global variable
‘.affylmGUIglobals’
bowtieDownload: no visible binding for global variable
‘affylmGUIenvironment’
bowtieDownload: no visible global function definition for
‘.bowtieGenomes’
bowtieDownload : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
bowtieDownload : onOK: no visible binding for global variable
‘.affylmGUIglobals’
bowtieDownload : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
bowtieGenomes: no visible binding for global variable
‘.affylmGUIglobals’
bowtieGenomes : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
bowtieGenomes : onOK: no visible binding for global variable
‘.affylmGUIglobals’
bowtieGenomes : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
bowtieGenomes: no visible binding for global variable
‘affylmGUIenvironment’
bowtieGenomes: no visible global function definition for ‘gunzip’
buildingLocalAnnotation: no visible binding for global variable
‘.affylmGUIglobals’
buildingLocalAnnotation : onOK: no visible binding for global variable
‘affylmGUIenvironment’
buildingLocalAnnotation : <anonymous>: no visible binding for global
variable ‘.affylmGUIglobals’
buildingLocalAnnotation: no visible binding for global variable
‘affylmGUIenvironment’
buildingLocalAnnotation: no visible global function definition for
‘NetAffxResource’
buildingLocalAnnotation : onOK: no visible binding for '<<-' assignment
to ‘ReturnNetaffx’
buildingLocalAnnotation : onOK: no visible binding for global variable
‘.affylmGUIglobals’
buildingLocalAnnotation : onCancel: no visible binding for global
variable ‘.affylmGUIglobals’
buildingLocalAnnotation: no visible binding for global variable
‘ReturnNetaffx’
buildingLocalAnnotation: no visible global function definition for
‘affxAnnotation’
buildingLocalAnnotation: no visible global function definition for
‘affxDescription’
buildingLocalAnnotation: no visible global function definition for
‘readAnnotation’
cdsDiff: no visible binding for global variable ‘affylmGUIenvironment’
cdsDiff: no visible global function definition for ‘readCufflinks’
cdsDiff: no visible global function definition for ‘CDS’
cdsDiff: no visible global function definition for ‘diffData’
cdsDiff: no visible binding for global variable ‘.affylmGUIglobals’
cdsDiff : onOK: no visible binding for '<<-' assignment to ‘ReturnVal’
cdsDiff : onOK: no visible binding for global variable
‘.affylmGUIglobals’
cdsDiff : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
cdsDiff : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
cdsDiff : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
cdsDiff: no visible binding for global variable ‘ReturnVal’
cdsDiff: no visible global function definition for ‘fpkm’
changeMenu: no visible binding for global variable ‘.affylmGUIglobals’
changeMenu: no visible binding for global variable
‘affylmGUIenvironment’
chimeraseq: no visible binding for global variable ‘.affylmGUIglobals’
chooseEDir: no visible binding for global variable ‘.affylmGUIglobals’
chooseInDir: no visible binding for global variable ‘.affylmGUIglobals’
chooseOutDir: no visible binding for global variable
‘.affylmGUIglobals’
colExtract: no visible binding for global variable ‘.affylmGUIglobals’
colExtract : onOK: no visible binding for global variable
‘affylmGUIenvironment’
colExtract : onOK: no visible binding for global variable
‘.affylmGUIglobals’
colExtract : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
colExtract: no visible binding for global variable
‘affylmGUIenvironment’
combineGeoMSF: no visible binding for global variable
‘.affylmGUIglobals’
combineGeoMSF : onOK: no visible binding for global variable
‘.affylmGUIglobals’
combineGeoMSF : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
combineGeoMSF: no visible binding for global variable
‘affylmGUIenvironment’
combining2eSet: no visible binding for global variable
‘.affylmGUIglobals’
ComputeContrasts: no visible binding for global variable
‘affylmGUIenvironment’
ComputeContrasts: no visible global function definition for
‘contrasts.fit’
ComputeContrasts: no visible global function definition for ‘eBayes’
ComputeLinearModelFit: no visible binding for global variable
‘affylmGUIenvironment’
ComputeLinearModelFit: no visible binding for global variable
‘.affylmGUIglobals’
ComputeLinearModelFit: no visible global function definition for
‘lm.series’
consistentFilters: no visible binding for global variable
‘.affylmGUIglobals’
consistentFilters: no visible binding for global variable
‘affylmGUIenvironment’
consistentFilters : onOK: no visible binding for '<<-' assignment to
‘ReturnFilter’
consistentFilters : onOK: no visible binding for global variable
‘.affylmGUIglobals’
consistentFilters : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
consistentFilters : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
consistentFilters: no visible binding for global variable
‘ReturnFilter’
consistentFilters : onOK: no visible binding for global variable
‘affylmGUIenvironment’
cosieWrapper: no visible binding for global variable
‘affylmGUIenvironment’
cosieWrapper: no visible binding for global variable
‘.affylmGUIglobals’
createDir: no visible binding for global variable
‘affylmGUIenvironment’
createGeoTarget: no visible binding for global variable
‘.affylmGUIglobals’
crosshybFilter: no visible binding for global variable
‘affylmGUIenvironment’
crosshybFilter: no visible binding for global variable
‘.affylmGUIglobals’
crosshybFilter : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
crosshybFilter : onOK: no visible binding for global variable
‘.affylmGUIglobals’
crosshybFilter : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
ctrtrtHeatmap: no visible binding for global variable
‘affylmGUIenvironment’
ctrtrtHeatmap: no visible binding for global variable
‘.affylmGUIglobals’
cuffdiff: no visible binding for global variable ‘affylmGUIenvironment’
cuffdiff: no visible binding for global variable ‘.affylmGUIglobals’
cuffdiff : onOK: no visible binding for global variable
‘affylmGUIenvironment’
cuffdiff : onOK: no visible binding for global variable
‘.affylmGUIglobals’
cuffdiff : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
cufflinks: no visible binding for global variable ‘.affylmGUIglobals’
cufflinks : onOK: no visible binding for global variable
‘affylmGUIenvironment’
cufflinks : onOK: no visible binding for global variable
‘.affylmGUIglobals’
cufflinks : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
cufflinks: no visible binding for global variable
‘affylmGUIenvironment’
cuffmerge: no visible binding for global variable ‘.affylmGUIglobals’
cuffmerge : onOK: no visible binding for global variable
‘affylmGUIenvironment’
cuffmerge : onOK: no visible binding for global variable
‘.affylmGUIglobals’
cuffmerge : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
cuffmerge: no visible binding for global variable
‘affylmGUIenvironment’
dabgFilter: no visible binding for global variable
‘affylmGUIenvironment’
dabgFilter: no visible binding for global variable ‘.affylmGUIglobals’
dabgFilter : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
dabgFilter : onOK: no visible binding for global variable
‘.affylmGUIglobals’
dabgFilter : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
dabgFilter : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
dabgFilter : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
dabgFilter: no visible binding for global variable ‘ReturnVal’
delete.ML: no visible binding for global variable
‘affylmGUIenvironment’
delete.ML: no visible binding for global variable ‘.affylmGUIglobals’
deleteLocalData: no visible binding for global variable
‘.affylmGUIglobals’
desCounts: no visible binding for global variable ‘.affylmGUIglobals’
desCounts : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
desCounts : onOK: no visible binding for global variable
‘.affylmGUIglobals’
desCounts : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
desCounts : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
desCounts : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
desCounts: no visible binding for global variable ‘ReturnVal’
DESeqInterface: no visible binding for global variable
‘affylmGUIenvironment’
DESeqInterface: no visible binding for global variable
‘.affylmGUIglobals’
DESeqInterface: no visible global function definition for
‘newCountDataSet’
DESeqInterface : .plotDispEsts: no visible global function definition
for ‘fitInfo’
DESeqInterface : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
DESeqInterface : onOK: no visible binding for global variable
‘.affylmGUIglobals’
DESeqInterface : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
DESeqInterface: no visible global function definition for ‘nbinomTest’
DESeqInterface : onOK: no visible binding for '<<-' assignment to
‘fcpVal’
DESeqInterface : onCancel: no visible binding for '<<-' assignment to
‘fcpVal’
DESeqInterface: no visible binding for global variable ‘fcpVal’
desGenes: no visible global function definition for
‘newCountDataSetFromHTSeqCount’
desGenes: no visible global function definition for ‘nbinomTest’
dexCounts: no visible binding for global variable ‘.affylmGUIglobals’
dexCounts : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
dexCounts : onOK: no visible binding for global variable
‘.affylmGUIglobals’
dexCounts : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
dexCounts : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
dexCounts : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
dexCounts: no visible binding for global variable ‘ReturnVal’
dfMAplot: no visible binding for global variable ‘.affylmGUIglobals’
dfMAplot : onOK: no visible binding for '<<-' assignment to ‘ReturnVal’
dfMAplot : onOK: no visible binding for global variable
‘.affylmGUIglobals’
dfMAplot : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
dfMAplot : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
dfMAplot: no visible binding for global variable ‘ReturnVal’
EDAbetweenLane: no visible binding for global variable
‘affylmGUIenvironment’
EDAbetweenLane: no visible binding for global variable
‘.affylmGUIglobals’
EDAbetweenLane: no visible global function definition for
‘newSeqExpressionSet’
EDAbetweenLane : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
EDAbetweenLane : onOK: no visible binding for global variable
‘.affylmGUIglobals’
EDAbetweenLane : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
EDAbetweenLane: no visible global function definition for
‘betweenLaneNormalization’
EDAbiasPlot: no visible binding for global variable
‘affylmGUIenvironment’
EDAbiasPlot: no visible binding for global variable ‘.affylmGUIglobals’
EDAbiasPlot: no visible global function definition for
‘newSeqExpressionSet’
EDAbiasPlot: no visible global function definition for ‘biasPlot’
EDAboxplot: no visible binding for global variable
‘affylmGUIenvironment’
EDAboxplot: no visible binding for global variable ‘.affylmGUIglobals’
EDAboxplot: no visible global function definition for
‘newSeqExpressionSet’
EDANtFreq: no visible binding for global variable
‘affylmGUIenvironment’
EDANtFreq: no visible binding for global variable ‘.affylmGUIglobals’
EDANtFreq : onOK: no visible binding for global variable
‘affylmGUIenvironment’
EDANtFreq : onOK: no visible binding for global variable
‘.affylmGUIglobals’
EDANtFreq : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
EDANtFreq: no visible global function definition for ‘plotNtFrequency’
EDAplotQuality: no visible binding for global variable
‘affylmGUIenvironment’
EDAplotQuality: no visible binding for global variable
‘.affylmGUIglobals’
EDAplotQuality: no visible global function definition for ‘plotQuality’
EDAreadNumber: no visible binding for global variable
‘affylmGUIenvironment’
EDAreadNumber: no visible binding for global variable
‘.affylmGUIglobals’
EDAwithinLane: no visible binding for global variable
‘affylmGUIenvironment’
EDAwithinLane: no visible binding for global variable
‘.affylmGUIglobals’
EDAwithinLane: no visible global function definition for
‘newSeqExpressionSet’
EDAwithinLane : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
EDAwithinLane : onOK: no visible binding for global variable
‘.affylmGUIglobals’
EDAwithinLane : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
EDAwithinLane : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
EDAwithinLane : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
EDAwithinLane: no visible binding for global variable ‘ReturnVal’
EDAwithinLane: no visible global function definition for
‘withinLaneNormalization’
EDAwithinLane: no visible global function definition for ‘biasPlot’
edgerInterface: no visible binding for global variable
‘affylmGUIenvironment’
edgerInterface: no visible binding for global variable
‘.affylmGUIglobals’
edgerInterface: no visible global function definition for ‘DGEList’
edgerInterface: no visible global function definition for
‘estimateCommonDisp’
edgerInterface: no visible global function definition for ‘getPriorN’
edgerInterface: no visible global function definition for
‘estimateTagwiseDisp’
edgerInterface : onOK: no visible binding for global variable
‘affylmGUIenvironment’
edgerInterface : onOK: no visible binding for global variable
‘.affylmGUIglobals’
edgerInterface : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
edgerInterface: no visible global function definition for ‘exactTest’
edgerInterface : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
edgerInterface : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
edgerInterface : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
edgerInterface: no visible binding for global variable ‘ReturnVal’
edgerInterface: no visible global function definition for ‘topTags’
edgerInterface: no visible global function definition for ‘plotSmear’
edgeRNorm: no visible binding for global variable ‘.affylmGUIglobals’
edgeRNorm: no visible binding for global variable
‘affylmGUIenvironment’
edgeRNorm: no visible global function definition for ‘DGEList’
edgeRNorm: no visible global function definition for
‘estimateCommonDisp’
edgeRNorm: no visible global function definition for ‘plotMDS.dge’
edgeRNorm: no visible global function definition for ‘calcNormFactors’
EG2probeset: no visible binding for global variable ‘.affylmGUIglobals’
EG2probeset: no visible binding for global variable
‘affylmGUIenvironment’
EG2probeset : OpenAFile: no visible binding for global variable
‘.affylmGUIglobals’
erankProdAltSpl: no visible binding for global variable
‘affylmGUIenvironment’
erankProdAltSpl: no visible binding for global variable
‘.affylmGUIglobals’
erankProdAltSpl : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
erankProdAltSpl : onOK: no visible binding for global variable
‘.affylmGUIglobals’
erankProdAltSpl : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
erankProdAltSpl: no visible binding for '<<-' assignment to ‘ReturnVal’
erankProdAltSpl : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
erankProdAltSpl: no visible global function definition for ‘RP’
erankProdAltSpl: no visible binding for global variable ‘ReturnVal’
erankProdAltSpl: no visible global function definition for ‘RPadvance’
erankProdAltSplFilter: no visible binding for global variable
‘affylmGUIenvironment’
erankProdAltSplFilter: no visible binding for global variable
‘.affylmGUIglobals’
erankProdAltSplFilter : onOK: no visible binding for global variable
‘affylmGUIenvironment’
erankProdAltSplFilter : <anonymous>: no visible binding for global
variable ‘.affylmGUIglobals’
eSet4meV: no visible binding for global variable ‘affylmGUIenvironment’
exonContrasts: no visible binding for global variable
‘affylmGUIenvironment’
exonContrasts: no visible global function definition for
‘contrasts.fit’
exonContrasts: no visible global function definition for ‘eBayes’
exonScaffold: no visible global function definition for ‘useMart’
exonScaffold: no visible global function definition for ‘useDataset’
exonScaffold: no visible global function definition for ‘getBM’
exonsSpecific2as: no visible binding for global variable
‘.affylmGUIglobals’
exonsSpecific2as: no visible binding for global variable
‘affylmGUIenvironment’
exonsSpecific2as: no visible global function definition for ‘useMart’
exonsSpecific2as: no visible global function definition for
‘useDataset’
exonsSpecific2as: no visible global function definition for ‘getBM’
exonsSpecific2as: no visible global function definition for
‘getSequence’
exonTopTableExtract: no visible binding for global variable
‘affylmGUIenvironment’
exonTopTableExtract: no visible binding for global variable
‘.affylmGUIglobals’
exonTopTableExtract : onOK: no visible binding for global variable
‘affylmGUIenvironment’
exonTopTableExtract : <anonymous>: no visible binding for global
variable ‘.affylmGUIglobals’
exportFASTA: no visible binding for global variable ‘.affylmGUIglobals’
exportFASTA : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
exportFASTA : onOK: no visible binding for global variable
‘.affylmGUIglobals’
exportFASTA : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
exportFASTA: no visible binding for global variable ‘hairpin’
ExportfeatureNames: no visible binding for global variable
‘.affylmGUIglobals’
ExportfeatureNames: no visible binding for global variable
‘affylmGUIenvironment’
ExportNormalizedExpressionValues: no visible binding for global
variable ‘affylmGUIenvironment’
ExportNormalizedExpressionValues1: no visible binding for global
variable ‘.affylmGUIglobals’
ExportNormalizedExpressionValues1: no visible binding for global
variable ‘affylmGUIenvironment’
extPckInfo: no visible binding for global variable
‘affylmGUIenvironment’
extPckInfo: no visible binding for global variable ‘.affylmGUIglobals’
extractAffyids: no visible binding for global variable
‘.affylmGUIglobals’
extractAffyids: no visible binding for global variable
‘affylmGUIenvironment’
extractAffyids : onOK: no visible binding for global variable
‘affylmGUIenvironment’
extractAffyids : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
extractAffyids : OpenAFile: no visible binding for global variable
‘.affylmGUIglobals’
extractAffyids: no visible global function definition for ‘lookUp’
extractAffyids: no visible binding for global variable
‘huex.annotation’
extractAffyids: no visible binding for global variable
‘moex.annotation’
extractAffyids: no visible binding for global variable
‘raex.annotation’
extractAffyids: no visible global function definition for ‘aafTableAnn’
extractAffyids: no visible global function definition for ‘aaf.handler’
extractAffyids : SaveHtmlTable: no visible global function definition
for ‘saveHTML’
extractmirTargets: no visible binding for global variable
‘.affylmGUIglobals’
extractmirTargets : onOK: no visible binding for global variable
‘affylmGUIenvironment’
extractmirTargets : onOK: no visible binding for global variable
‘.affylmGUIglobals’
extractmirTargets : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
extractmirTargets: no visible binding for global variable
‘affylmGUIenvironment’
fastQC: no visible binding for global variable ‘affylmGUIenvironment’
filteringmiRtargets: no visible binding for global variable
‘.affylmGUIglobals’
filteringmiRtargets : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
filteringmiRtargets : onOK: no visible binding for global variable
‘.affylmGUIglobals’
filteringmiRtargets : <anonymous>: no visible binding for global
variable ‘.affylmGUIglobals’
filteringmiRtargets: no visible global function definition for
‘RmiR.Hs.miRNA_dbconn’
filteringmiRtargets: no visible global function definition for ‘lookUp’
filteringTable: no visible binding for global variable
‘.affylmGUIglobals’
fusionfilter: no visible binding for global variable
‘.affylmGUIglobals’
fusionfilter : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
fusionfilter : onOK: no visible binding for global variable
‘.affylmGUIglobals’
fusionfilter : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
fusionNS: no visible binding for global variable ‘.affylmGUIglobals’
fusionNS: no visible binding for global variable ‘raw.fusions’
fusionpeptides: no visible binding for global variable
‘.affylmGUIglobals’
fusionpeptides: possible error in fusionPeptides(my.fset, which.isoform
= 1, donor.up = 50, acceptor.down = 50): unused arguments
(which.isoform = 1, donor.up = 50, acceptor.down = 50)
fusionpeptides: no visible binding for global variable ‘my.fset’
geneDiff: no visible binding for global variable ‘affylmGUIenvironment’
geneDiff: no visible global function definition for ‘readCufflinks’
geneDiff: no visible global function definition for ‘diffData’
geneDiff: no visible binding for global variable ‘.affylmGUIglobals’
geneDiff : onOK: no visible binding for '<<-' assignment to ‘ReturnVal’
geneDiff : onOK: no visible binding for global variable
‘.affylmGUIglobals’
geneDiff : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
geneDiff : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
geneDiff : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
geneDiff: no visible binding for global variable ‘ReturnVal’
geneDiff: no visible global function definition for ‘getGenes’
geneDiff: no visible global function definition for ‘fpkm’
geneExonLibs: no visible binding for global variable
‘.affylmGUIglobals’
geneExonLibs: no visible binding for global variable
‘affylmGUIenvironment’
genomePlot: no visible binding for global variable ‘.affylmGUIglobals’
genomePlot: no visible binding for global variable
‘affylmGUIenvironment’
genomePlot : onOK: no visible binding for global variable
‘affylmGUIenvironment’
genomePlot : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
genomePlot: no visible global function definition for ‘useMart’
genomePlot: no visible global function definition for ‘getBM’
genomePlot: no visible global function definition for ‘DisplayPars’
genomePlot: no visible global function definition for ‘makeGene’
genomePlot: no visible global function definition for ‘makeTranscript’
genomePlot: no visible global function definition for
‘makeRectangleOverlay’
genomePlot: no visible global function definition for ‘gdPlot’
genomePlot: no visible binding for global variable
‘crosshybraex.annotation’
genomeStudioReformat: no visible binding for global variable
‘.affylmGUIglobals’
getNGSannotation: no visible binding for '<<-' assignment to
‘ReturnAnn’
getNGSannotation: no visible binding for global variable
‘.affylmGUIglobals’
getNGSannotation : onOK: no visible binding for '<<-' assignment to
‘ReturnAnn’
getNGSannotation : onOK: no visible binding for global variable
‘.affylmGUIglobals’
getNGSannotation : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
getNGSannotation : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
getNGSannotation: no visible binding for global variable ‘ReturnAnn’
getNGSannotation: no visible global function definition for ‘useMart’
getNGSannotation: no visible global function definition for
‘getAnnotation’
getNGSannotation: no visible binding for global variable
‘affylmGUIenvironment’
GetNormalizationMethod: no visible binding for global variable
‘.affylmGUIglobals’
GetNormalizationMethod : onCancel: no visible binding for global
variable ‘.affylmGUIglobals’
GetNormalizationMethod : onOK: no visible binding for global variable
‘.affylmGUIglobals’
GetNormalizationMethod : <anonymous>: no visible binding for global
variable ‘.affylmGUIglobals’
GOenrichment: no visible binding for global variable
‘.affylmGUIglobals’
GOenrichment: no visible binding for global variable
‘affylmGUIenvironment’
GOenrichment : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
GOenrichment : onOK: no visible binding for global variable
‘.affylmGUIglobals’
GOenrichment : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
GOenrichment : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
GOenrichment: no visible binding for global variable ‘ReturnVal’
GOenrichment : OpenAFile: no visible binding for global variable
‘.affylmGUIglobals’
GOenrichment: no visible binding for global variable ‘huex.annotation’
GOenrichment: no visible binding for global variable ‘moex.annotation’
GOenrichment: no visible binding for global variable ‘raex.annotation’
GOenrichment: no visible global function definition for ‘lookUp’
GOenrichment: no visible global function definition for ‘hyperGTest’
GOenrichment: no visible global function definition for
‘universeCounts’
GOenrichment: no visible global function definition for ‘pvalues’
GOenrichment: no visible global function definition for ‘geneIds’
GOenrichment: no visible global function definition for
‘universeMappedCount’
GOenrichment: no visible global function definition for ‘conditional<-’
GOenrichment: no visible global function definition for ‘GOGraph’
GOenrichment: no visible binding for global variable ‘GOBPPARENTS’
GOenrichment: no visible binding for global variable ‘GOMFPARENTS’
GOenrichment: no visible binding for global variable ‘GOCCPARENTS’
GOenrichment: no visible global function definition for ‘nodes’
GOenrichment: no visible global function definition for ‘makeNodeAttrs’
goseqInterface: no visible binding for global variable
‘.affylmGUIglobals’
goseqInterface: no visible binding for global variable
‘affylmGUIenvironment’
goseqInterface: no visible global function definition for ‘nullp’
goseqInterface: no visible global function definition for ‘goseq’
goseqInterface : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
goseqInterface : onOK: no visible binding for global variable
‘.affylmGUIglobals’
goseqInterface : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
importfusions: no visible binding for global variable
‘.affylmGUIglobals’
importfusions : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
importfusions : onOK: no visible binding for global variable
‘.affylmGUIglobals’
importfusions : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
initialize.extAffylmGUI: no visible binding for global variable
‘affylmGUIenvironment’
initialize.extAffylmGUI: no visible binding for global variable
‘.affylmGUIglobals’
inspecting.one.splice.index: no visible binding for global variable
‘.affylmGUIglobals’
inspecting.one.splice.index: no visible binding for global variable
‘affylmGUIenvironment’
inspecting.one.splice.index : onOK: no visible binding for global
variable ‘affylmGUIenvironment’
inspecting.one.splice.index : <anonymous>: no visible binding for
global variable ‘.affylmGUIglobals’
inspecting.splice.index: no visible binding for global variable
‘.affylmGUIglobals’
inspecting.splice.index: no visible binding for global variable
‘affylmGUIenvironment’
intensityFilter: no visible binding for global variable
‘.affylmGUIglobals’
intensityFilter : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
intensityFilter : onOK: no visible binding for global variable
‘.affylmGUIglobals’
intensityFilter : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
intensityFilter : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
intensityFilter : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
intensityFilter: no visible binding for global variable ‘ReturnVal’
intensityFilter: no visible global function definition for ‘pOverA’
intensityFilter: no visible global function definition for ‘filterfun’
intensityFilter: no visible global function definition for ‘genefilter’
intronicBg: no visible binding for global variable
‘affylmGUIenvironment’
intronicBg: no visible binding for global variable ‘.affylmGUIglobals’
intronicBg: no visible global function definition for ‘plotDensity’
intronicBg : onOK: no visible binding for global variable
‘affylmGUIenvironment’
intronicBg : onOK: no visible binding for global variable
‘.affylmGUIglobals’
intronicBg : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
IPAlistFilter: no visible binding for global variable
‘affylmGUIenvironment’
IPAlistFilter: no visible binding for global variable
‘.affylmGUIglobals’
IPAlistFilter: no visible global function definition for ‘lookUp’
IPAlistFilter: no visible binding for global variable ‘huex.annotation’
IPAlistFilter: no visible binding for global variable ‘moex.annotation’
IPAlistFilter: no visible binding for global variable ‘raex.annotation’
iqrFilter: no visible binding for global variable ‘.affylmGUIglobals’
iqrFilter : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
iqrFilter : onOK: no visible binding for global variable
‘.affylmGUIglobals’
iqrFilter : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
iqrFilter: no visible global function definition for ‘filterfun’
iqrFilter: no visible global function definition for ‘genefilter’
isoDiff: no visible binding for global variable ‘affylmGUIenvironment’
isoDiff: no visible global function definition for ‘readCufflinks’
isoDiff: no visible global function definition for ‘isoforms’
isoDiff: no visible global function definition for ‘diffData’
isoDiff: no visible binding for global variable ‘.affylmGUIglobals’
isoDiff : onOK: no visible binding for '<<-' assignment to ‘ReturnVal’
isoDiff : onOK: no visible binding for global variable
‘.affylmGUIglobals’
isoDiff : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
isoDiff : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
isoDiff : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
isoDiff: no visible binding for global variable ‘ReturnVal’
isoDiff: no visible global function definition for ‘fpkm’
javaFolder: no visible binding for global variable ‘.affylmGUIglobals’
javaFolder: no visible binding for global variable
‘affylmGUIenvironment’
largedatasetNorm: no visible binding for global variable
‘affylmGUIenvironment’
largedatasetNorm: no visible binding for global variable
‘.affylmGUIglobals’
largedatasetNorm : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
largedatasetNorm : onOK: no visible binding for global variable
‘.affylmGUIglobals’
largedatasetNorm : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
largedatasetNorm: no visible global function definition for
‘normalize.loess’
largedatasetNorm: no visible global function definition for
‘normalize.quantiles’
largedatasetNorm: no visible global function definition for
‘normalize.qspline’
libraryFilesDir: no visible binding for global variable
‘.affylmGUIglobals’
limma2paired: no visible binding for global variable
‘affylmGUIenvironment’
limma2paired: no visible binding for global variable
‘.affylmGUIglobals’
limma2paired: no visible global function definition for
‘duplicateCorrelation’
limma2paired: no visible global function definition for ‘lmFit’
limma2paired: no visible global function definition for ‘eBayes’
limma2paired : onOK: no visible binding for global variable
‘.affylmGUIglobals’
limma2paired : onHelp: possible error in help("topTable", htmlhelp =
TRUE): unused argument (htmlhelp = TRUE)
limma2paired : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
limma2paired : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
limma2paired: no visible global function definition for ‘lookUp’
limma2paired: no visible binding for global variable ‘huex.annotation’
limma2paired: no visible binding for global variable ‘moex.annotation’
limma2paired: no visible binding for global variable ‘raex.annotation’
limma2paired: no visible binding for global variable ‘annlib’
limma2paired: no visible global function definition for ‘toptable’
limmaExons: no visible binding for global variable
‘affylmGUIenvironment’
limmaExons: no visible binding for global variable ‘.affylmGUIglobals’
limmaExons: no visible global function definition for ‘lm.series’
listFilter: no visible binding for global variable
‘affylmGUIenvironment’
listFilter: no visible binding for global variable ‘.affylmGUIglobals’
listFilter : OpenAFile: no visible binding for global variable
‘.affylmGUIglobals’
log2Conversion: no visible binding for global variable
‘affylmGUIenvironment’
log2Conversion: no visible binding for global variable
‘.affylmGUIglobals’
makeBED15: no visible binding for global variable ‘.affylmGUIglobals’
makeGCcontent: no visible binding for global variable ‘Hsapiens’
makeGCcontent: no visible binding for global variable ‘Mmusculus’
makeGCcontent: no visible binding for global variable ‘Rnorvegicus’
makeGeneScaffold: no visible binding for global variable ‘chrLength’
makeGeneScaffold: no visible global function definition for
‘browserSession’
makeGeneScaffold: no visible global function definition for
‘ucscTableQuery’
makeGeneScaffold: no visible global function definition for
‘tableName<-’
makeGeneScaffold: no visible global function definition for ‘getTable’
makeGeneScaffold: no visible global function definition for
‘GRangesForUCSCGenome’
mapping2ensembl: no visible binding for global variable
‘.affylmGUIglobals’
mapping2ensembl: no visible binding for global variable
‘affylmGUIenvironment’
mapping2ensembl: no visible global function definition for ‘useMart’
mapping2ensembl: no visible global function definition for ‘useDataset’
mapping2ensembl: no visible global function definition for
‘getSequence’
mapping2exon: no visible binding for global variable
‘.affylmGUIglobals’
mapping2exon: no visible binding for global variable
‘affylmGUIenvironment’
mapping2exon: no visible global function definition for
‘read.DNAStringSet’
mapping2exon: no visible global function definition for ‘writeFASTA’
mapping2RefSeq: no visible binding for global variable
‘.affylmGUIglobals’
mapping2RefSeq: no visible binding for global variable
‘affylmGUIenvironment’
mapping2RefSeq: no visible global function definition for
‘read.DNAStringSet’
mapping2RefSeq : map2rs: no visible global function definition for
‘lookUp’
masigpro: no visible binding for global variable ‘affylmGUIenvironment’
masigpro: no visible binding for global variable ‘.affylmGUIglobals’
masigpro: no visible global function definition for
‘make.design.matrix’
masigpro : onOK: no visible binding for global variable
‘.affylmGUIglobals’
masigpro : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
masigpro : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
masigpro: no visible global function definition for ‘p.vector’
masigpro: no visible global function definition for ‘T.fit’
masigpro: no visible global function definition for ‘get.siggenes’
masigpro.edesign: no visible binding for global variable
‘affylmGUIenvironment’
masigpro.edesign: no visible binding for global variable
‘.affylmGUIglobals’
masigpro.edesign : onClose: no visible binding for global variable
‘.affylmGUIglobals’
masigpro.edesign : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
masigpro.view: no visible binding for global variable
‘affylmGUIenvironment’
masigpro.view: no visible binding for global variable
‘.affylmGUIglobals’
masigpro.view : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
masigpro.view : onOK: no visible binding for global variable
‘.affylmGUIglobals’
masigpro.view : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
masigpro.view : plotFunction: no visible binding for global variable
‘include’
masigpro.view: no visible global function definition for ‘vennCounts’
masigpro.view : onOK: no visible binding for global variable
‘affylmGUIenvironment’
masigpro.view: no visible global function definition for ‘PlotGroups’
metaArrayIC: no visible binding for global variable
‘affylmGUIenvironment’
metaArrayIC: no visible binding for global variable ‘.affylmGUIglobals’
metaArrayIC: no visible global function definition for ‘intcor’
metaArrayMerge : OpenAFile: no visible binding for global variable
‘.affylmGUIglobals’
metaArrayMerge: no visible binding for global variable
‘affylmGUIenvironment’
metaArrayMerge: no visible binding for global variable
‘.affylmGUIglobals’
metaArrayMerge : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
metaArrayMerge : onOK: no visible binding for global variable
‘.affylmGUIglobals’
metaArrayMerge : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
metaArrayMerge: no visible global function definition for ‘mergeExprs’
meVDownload: no visible binding for global variable ‘.affylmGUIglobals’
meVDownload: no visible binding for global variable
‘affylmGUIenvironment’
meVDownload : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
meVDownload : onOK: no visible binding for global variable
‘.affylmGUIglobals’
meVDownload : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
midasFilter: no visible binding for global variable
‘affylmGUIenvironment’
midasFilter: no visible binding for global variable ‘.affylmGUIglobals’
midasFilter : onOK: no visible binding for global variable
‘affylmGUIenvironment’
midasFilter : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
miRNAbowtieRun : onOK: no visible binding for global variable
‘affylmGUIenvironment’
miRNAbowtieRun: no visible binding for global variable
‘affylmGUIenvironment’
miRNAbowtieRun : onOK: no visible binding for '<<-' assignment to
‘bowtieVal’
miRNAbowtieRun : onCancel: no visible binding for '<<-' assignment to
‘bowtieVal’
miRNAbowtieRun: no visible binding for global variable ‘bowtieVal’
ML.edesign: no visible binding for global variable
‘affylmGUIenvironment’
ML.edesign: no visible binding for global variable ‘.affylmGUIglobals’
ML.edesign : onClose: no visible binding for global variable
‘.affylmGUIglobals’
ML.edesign : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
mRNAbowtieRun: no visible binding for global variable
‘affylmGUIenvironment’
mRNAbowtieRun : onOK: no visible binding for global variable
‘affylmGUIenvironment’
mRNAbowtieRun : onOK: no visible binding for '<<-' assignment to
‘bowtieVal’
mRNAbowtieRun : onCancel: no visible binding for '<<-' assignment to
‘bowtieVal’
mRNAbowtieRun: no visible binding for global variable ‘bowtieVal’
mRNAmiRCor: no visible binding for global variable ‘.affylmGUIglobals’
mRNAmiRCor: no visible binding for global variable
‘affylmGUIenvironment’
mRNAmiRCor : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
mRNAmiRCor : onOK: no visible binding for global variable
‘.affylmGUIglobals’
mRNAmiRCor : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
mRNAmiRCor : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
mRNAmiRCor : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
mRNAmiRCor: no visible binding for global variable ‘ReturnVal’
mRNAmiRCor : .OpenAmiRFile: no visible binding for global variable
‘.affylmGUIglobals’
mRNAmiRCor: no visible global function definition for ‘PlotGroups’
mRNAmiRCor: possible error in Try(tkmessageBox(title = "Filtering by
correlation", message = "The data set in oneChannelGUI and the miR
data have the samples organized in different way!\nPlease modify the
miRdata file to have the same samples organization as in the Target
name of the dataset load in oneChannelGUI."), type = "error"): unused
argument (type = "error")
mRNAmiRCor: possible error in Try(tkmessageBox(title = "Filtering by
correlation", message = "The data set in oneChannelGUI and the miR
data do not contain the same number of samples!"), type = "error"):
unused argument (type = "error")
myExpresso: no visible binding for global variable
‘affylmGUIenvironment’
myExpresso: no visible binding for global variable ‘.affylmGUIglobals’
myExpresso: no visible global function definition for ‘expresso’
ncScaffold: no visible global function definition for ‘useMart’
ncScaffold: no visible global function definition for ‘useDataset’
ncScaffold: no visible global function definition for ‘getBM’
ncScaffold: no visible global function definition for ‘writeFASTA’
ncScaffold: no visible global function definition for ‘readFASTA’
NewLimmaFile: no visible binding for global variable
‘affylmGUIenvironment’
NewLimmaFileNGS: no visible binding for global variable
‘affylmGUIenvironment’
ngsperlDownload: no visible binding for global variable
‘.affylmGUIglobals’
ngsperlDownload: no visible binding for global variable
‘affylmGUIenvironment’
NGSreformat: no visible binding for global variable
‘affylmGUIenvironment’
NGSreformat : onOK: no visible binding for global variable
‘affylmGUIenvironment’
NormalizeNow: no visible binding for global variable
‘affylmGUIenvironment’
NormalizeNow: no visible binding for global variable
‘.affylmGUIglobals’
NormalizeNow: no visible global function definition for ‘rma’
NormalizeNow: no visible global function definition for ‘gcrma’
normBoxplot: no visible binding for global variable
‘affylmGUIenvironment’
normBoxplot: no visible binding for global variable ‘.affylmGUIglobals’
ocPlotHist: no visible binding for global variable
‘affylmGUIenvironment’
ocPlotHist: no visible binding for global variable ‘.affylmGUIglobals’
ocPlotHist : plotHist: no visible global function definition for
‘plotDensity’
ocPlotHist : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
ocPlotHist : onOK: no visible binding for global variable
‘.affylmGUIglobals’
ocPlotHist : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
ocPlotPCA: no visible binding for global variable
‘affylmGUIenvironment’
ocPlotPCA: no visible binding for global variable ‘.affylmGUIglobals’
ocPlotPCA : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
ocPlotPCA : onOK: no visible binding for global variable
‘.affylmGUIglobals’
ocPlotPCA : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
oneChannelGUI: no visible binding for global variable
‘affylmGUIenvironment’
oneChannelGUI: no visible binding for global variable
‘.affylmGUIglobals’
OpenAFile: no visible binding for global variable ‘.affylmGUIglobals’
OpenAGeoFile: no visible binding for global variable
‘.affylmGUIglobals’
OpenAGeoFile: no visible binding for global variable
‘affylmGUIenvironment’
OpenALimmaFile: no visible binding for global variable
‘affylmGUIenvironment’
OpenBeadStudioFiles : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenBeadStudioFiles: no visible binding for global variable
‘affylmGUIenvironment’
OpenCDFandTargetsfiles : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenCDFandTargetsfiles: no visible binding for global variable
‘affylmGUIenvironment’
OpenCDFandTargetsfiles: no visible global function definition for
‘ReadAffy’
OpenExonandTargetsfiles : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenExonandTargetsfiles: no visible binding for global variable
‘affylmGUIenvironment’
OpenExonandTargetsfiles: no visible binding for '<<-' assignment to
‘ReturnValX’
OpenExonandTargetsfiles : onOK: no visible binding for '<<-' assignment
to ‘ReturnValX’
OpenExonandTargetsfiles: no visible binding for global variable
‘ReturnValX’
OpenExonandTargetsfiles: no visible binding for global variable
‘glibVal’
OpenGeoFiles : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenGeoFiles: no visible binding for global variable
‘affylmGUIenvironment’
OpenGeoFiles: no visible binding for global variable ‘geoVSbioc’
OpenLargefiles : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenLargefiles: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRanalyserfiles : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRanalyserfiles: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRBam : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRBam: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRExpress : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRExpress: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRProfiles : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRProfiles: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRShrimp : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenmiRShrimp: no visible binding for global variable
‘affylmGUIenvironment’
OpenmRNABam : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenmRNABam: no visible binding for global variable
‘affylmGUIenvironment’
OpenmRNABam: no visible global function definition for
‘readGAlignmentsFromBam’
OpenmRNABam: no visible global function definition for ‘matchMatrix’
OpenNgsfiles : onOK: no visible binding for global variable
‘affylmGUIenvironment’
OpenNgsfiles: no visible binding for global variable
‘affylmGUIenvironment’
openPdf: no visible binding for global variable ‘.affylmGUIglobals’
openPdf : onOK: no visible binding for global variable
‘.affylmGUIglobals’
openPdf : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
plierToZero: no visible binding for global variable
‘affylmGUIenvironment’
plierToZero: no visible binding for global variable ‘.affylmGUIglobals’
plotcoverage: no visible binding for global variable
‘.affylmGUIglobals’
plotcoverage : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
plotcoverage : onOK: no visible binding for global variable
‘.affylmGUIglobals’
plotcoverage : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
plotcoverage: no visible binding for global variable ‘my.fset’
plotDE.exons: no visible binding for global variable
‘.affylmGUIglobals’
plotDE.exons : onOK: no visible binding for global variable
‘.affylmGUIglobals’
plotDE.exons : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
plotDE.exons : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
plotDE.exons: no visible global function definition for ‘plotDEXSeq’
plotDE.exons: no visible binding for global variable ‘res.exons’
plotGO: no visible binding for global variable ‘affylmGUIenvironment’
plotGO: no visible binding for global variable ‘.affylmGUIglobals’
plotGO : onOK: no visible binding for global variable
‘affylmGUIenvironment’
plotGO : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
plotGO : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
plotGO : onOK: no visible binding for global variable
‘.affylmGUIglobals’
plotGO: no visible global function definition for ‘GOGraph’
plotGO: no visible binding for global variable ‘GOBPPARENTS’
plotGO: no visible global function definition for ‘nodes’
plotGO: no visible global function definition for ‘removeNode’
plotGO: no visible global function definition for ‘getGOTerm’
plotGO: no visible binding for global variable ‘GOMFPARENTS’
plotGO: no visible binding for global variable ‘GOCCPARENTS’
PlotOptionsv1: no visible binding for global variable
‘.affylmGUIglobals’
PlotOptionsv1 : onOK: no visible binding for global variable
‘.affylmGUIglobals’
PlotOptionsv1 : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
plotVariantSI: no visible binding for global variable
‘.affylmGUIglobals’
plotVariantSI : onOK: no visible binding for global variable
‘affylmGUIenvironment’
plotVariantSI : onOK: no visible binding for global variable
‘.affylmGUIglobals’
plotVariantSI : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
plotVariantSI: no visible binding for global variable
‘affylmGUIenvironment’
plotVariantSI: no visible global function definition for ‘GenomicData’
plotVariantSI: no visible global function definition for
‘browserSession’
plotVariantSI: no visible global function definition for ‘track<-’
plotVariantSI: no visible global function definition for ‘browserView’
qcMDS: no visible binding for global variable ‘affylmGUIenvironment’
qcMDS: no visible binding for global variable ‘.affylmGUIglobals’
qcMDS: no visible global function definition for ‘DGEList’
qcMDS: no visible global function definition for ‘estimateCommonDisp’
qcMDS: no visible global function definition for ‘plotMDS.DGEList’
rankingConversion: no visible binding for global variable
‘affylmGUIenvironment’
rankingConversion: no visible binding for global variable
‘.affylmGUIglobals’
rankProd: no visible binding for global variable ‘affylmGUIenvironment’
rankProd: no visible binding for global variable ‘.affylmGUIglobals’
rankProd : onOK: no visible binding for '<<-' assignment to ‘ReturnVal’
rankProd : onOK: no visible binding for global variable
‘.affylmGUIglobals’
rankProd : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
rankProd : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
rankProd : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
rankProd: no visible binding for global variable ‘ReturnVal’
rankProd: no visible global function definition for ‘RP’
rankProd: no visible global function definition for ‘RPadvance’
rankProd: no visible global function definition for ‘topGene’
rankProd: no visible global function definition for ‘lookUp’
rankProd: no visible global function definition for ‘getDataEnv’
rawBoxplotPN: no visible binding for global variable
‘affylmGUIenvironment’
rawBoxplotPN: no visible binding for global variable
‘.affylmGUIglobals’
rawpCheck: no visible binding for global variable
‘affylmGUIenvironment’
rawpCheck: no visible binding for global variable ‘.affylmGUIglobals’
Reads2logos: no visible binding for global variable ‘.affylmGUIglobals’
Reads2logos: no visible binding for global variable
‘affylmGUIenvironment’
Reads2logos : onOK: no visible binding for global variable
‘affylmGUIenvironment’
Reads2logos : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
Reads2logos : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
Reads2logos : onOK: no visible binding for global variable
‘.affylmGUIglobals’
recoverUnfiltered: no visible binding for global variable
‘.affylmGUIglobals’
recoverUnfiltered: no visible binding for global variable
‘affylmGUIenvironment’
recoverUnfiltered: no visible binding for global variable ‘x’
recoverUnfiltered: no visible binding for global variable ‘x.exon’
refiningPeaks: no visible binding for global variable
‘affylmGUIenvironment’
refiningPeaks: no visible binding for global variable
‘.affylmGUIglobals’
refiningPeaks : onOK: no visible binding for global variable
‘affylmGUIenvironment’
refiningPeaks : onOK: no visible binding for global variable
‘.affylmGUIglobals’
refiningPeaks : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
reformatGdl: no visible binding for global variable ‘.affylmGUIglobals’
reformatGdl: no visible binding for global variable
‘affylmGUIenvironment’
reformatGdl : onOK: no visible binding for global variable
‘affylmGUIenvironment’
reformatGdl : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
refseqDownload: no visible binding for global variable
‘.affylmGUIglobals’
refseqDownload: no visible binding for global variable
‘affylmGUIenvironment’
refseqDownload: no visible global function definition for ‘readFASTA’
refseqDownload: no visible global function definition for ‘writeFASTA’
retrieveMirTargets: no visible binding for global variable
‘.affylmGUIglobals’
retrieveMirTargets : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
retrieveMirTargets : onOK: no visible binding for global variable
‘.affylmGUIglobals’
retrieveMirTargets : <anonymous>: no visible binding for global
variable ‘.affylmGUIglobals’
retrieveMirTargets : onOK: no visible binding for global variable
‘affylmGUIenvironment’
retrieveMirTargets: no visible binding for global variable
‘affylmGUIenvironment’
retrieveMirTargets: no visible global function definition for
‘RmiR.Hs.miRNA_dbconn’
retrieveMirTargets: no visible global function definition for
‘getSYMBOL’
retrievePSRseq: no visible binding for global variable
‘.affylmGUIglobals’
retrievePSRseq: no visible binding for global variable
‘affylmGUIenvironment’
retrievePSRseq1gid: no visible binding for global variable
‘.affylmGUIglobals’
retrievePSRseq1gid: no visible binding for global variable
‘affylmGUIenvironment’
retrievePSRseq1gid : onOK: no visible binding for global variable
‘affylmGUIenvironment’
retrievePSRseq1gid : <anonymous>: no visible binding for global
variable ‘.affylmGUIglobals’
reviqrFilter: no visible binding for global variable
‘.affylmGUIglobals’
reviqrFilter : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
reviqrFilter : onOK: no visible binding for global variable
‘.affylmGUIglobals’
reviqrFilter : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
reviqrFilter: no visible global function definition for ‘filterfun’
reviqrFilter: no visible global function definition for ‘genefilter’
RmiRInterface: no visible binding for global variable
‘.affylmGUIglobals’
RmiRInterface : onOK: no visible binding for global variable
‘.affylmGUIglobals’
RmiRInterface : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
RmiRInterface : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
RmiRInterface: no visible global function definition for ‘read.mir’
runningJetta: no visible binding for global variable
‘.affylmGUIglobals’
runningJetta: no visible binding for global variable
‘affylmGUIenvironment’
runningJetta: no visible binding for global variable ‘tmp’
runningJetta : onOK: no visible binding for global variable
‘.affylmGUIglobals’
runningJetta : onOK: no visible binding for global variable
‘affylmGUIenvironment’
runningJetta : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
runningJetta : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
runningJetta: no visible global function definition for ‘jetta.do.mads’
runningJetta: no visible global function definition for
‘jetta.read.expression’
runningJetta: no visible global function definition for
‘jetta.read.mads.output’
sample.size.evaluation: no visible binding for global variable
‘affylmGUIenvironment’
sample.size.evaluation: no visible binding for global variable
‘.affylmGUIglobals’
sample.size.evaluation : onOK: no visible binding for global variable
‘affylmGUIenvironment’
sample.size.evaluation : <anonymous>: no visible binding for global
variable ‘.affylmGUIglobals’
sample.size.evaluation : common.sd: no visible binding for global
variable ‘affylmGUIenvironment’
sample.size.evaluation : onCancel: no visible binding for global
variable ‘.affylmGUIglobals’
sample.size.evaluation : onOK: no visible binding for global variable
‘.affylmGUIglobals’
sample.size.evaluation: no visible global function definition for
‘mt.teststat’
sample.size.evaluation: no visible global function definition for
‘mt.rawp2adjp’
sample.size.evaluation: no visible global function definition for
‘ssize’
sample.size.evaluation: no visible global function definition for
‘ssize.plot’
sample.size.evaluation: no visible global function definition for
‘delta’
sample.size.evaluation1: no visible binding for global variable
‘affylmGUIenvironment’
sample.size.evaluation1: no visible binding for global variable
‘.affylmGUIglobals’
sample.size.evaluation1 : onCancel: no visible binding for global
variable ‘.affylmGUIglobals’
sample.size.evaluation1 : onOK: no visible binding for global variable
‘.affylmGUIglobals’
sample.size.evaluation1 : <anonymous>: no visible binding for global
variable ‘.affylmGUIglobals’
sample.size.evaluation1 : common.sd: no visible binding for global
variable ‘affylmGUIenvironment’
sample.size.evaluation1: no visible global function definition for
‘sampleSize.randomized’
sample.size.evaluation1: no visible global function definition for
‘power.randomized’
SaveAsLimmaFile: no visible binding for global variable
‘.affylmGUIglobals’
SaveAsLimmaFile: no visible binding for global variable
‘affylmGUIenvironment’
SaveLimmaFile: no visible binding for global variable
‘affylmGUIenvironment’
SaveLimmaFile: no visible binding for global variable
‘.affylmGUIglobals’
setBinDir: no visible binding for global variable ‘.affylmGUIglobals’
setBinDir: no visible binding for global variable
‘affylmGUIenvironment’
SetED: no visible binding for global variable ‘.affylmGUIglobals’
showDataset: no visible binding for global variable ‘.affylmGUIglobals’
showDataset: no visible binding for global variable
‘affylmGUIenvironment’
showDataset: no visible global function definition for ‘cdfName’
showTopTable: no visible binding for global variable
‘affylmGUIenvironment’
showTopTable: no visible global function definition for ‘eBayes’
showTopTable : onHelp: possible error in help("topTable", htmlhelp =
TRUE): unused argument (htmlhelp = TRUE)
showTopTable: no visible global function definition for ‘lookUp’
showTopTable: no visible binding for global variable ‘huex.annotation’
showTopTable: no visible binding for global variable ‘moex.annotation’
showTopTable: no visible binding for global variable ‘raex.annotation’
siggenes: no visible binding for global variable ‘affylmGUIenvironment’
siggenes: no visible binding for global variable ‘.affylmGUIglobals’
siggenes : onOK: no visible binding for global variable
‘affylmGUIenvironment’
siggenes : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
siggenes: no visible global function definition for ‘lookUp’
simFilter: no visible binding for global variable ‘.affylmGUIglobals’
simFilter : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
spliceIndex: no visible binding for global variable
‘affylmGUIenvironment’
spliceIndex: no visible binding for global variable ‘.affylmGUIglobals’
standAloneBuildingLocalAnnotation: no visible global function
definition for ‘NetAffxResource’
standAloneBuildingLocalAnnotation: no visible global function
definition for ‘affxAnnotation’
standAloneBuildingLocalAnnotation: no visible global function
definition for ‘affxDescription’
standAloneBuildingLocalAnnotation: no visible global function
definition for ‘readAnnotation’
startmeV: no visible binding for global variable ‘affylmGUIenvironment’
startmeV: no visible binding for global variable ‘.affylmGUIglobals’
targetWidget: no visible binding for global variable
‘.affylmGUIglobals’
targetWidget: possible error in sub("^/?([^/]*/)*", "", widgetfiles,
extended = TRUE): unused argument (extended = TRUE)
targetWidget: no visible global function definition for
‘read.phenoData’
templA: no visible binding for global variable ‘affylmGUIenvironment’
templA: no visible binding for global variable ‘.affylmGUIglobals’
templA : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
templA : onOK: no visible binding for global variable
‘.affylmGUIglobals’
templA : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
templA: no visible binding for global variable ‘huex.annotation’
templA: no visible binding for global variable ‘moex.annotation’
templA: no visible binding for global variable ‘raex.annotation’
tophat: no visible binding for global variable ‘.affylmGUIglobals’
tophat : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
tophat : onOK: no visible binding for global variable
‘.affylmGUIglobals’
tophat : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
tophat : onOK: no visible binding for global variable
‘affylmGUIenvironment’
tophat: no visible binding for global variable ‘affylmGUIenvironment’
tophatrun: no visible binding for global variable ‘.affylmGUIglobals’
tophatrun : onOK: no visible binding for global variable
‘affylmGUIenvironment’
tophatrun : onOK: no visible binding for global variable
‘.affylmGUIglobals’
tophatrun : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
tophatrun: no visible binding for global variable
‘affylmGUIenvironment’
topTable.exons: no visible binding for global variable
‘.affylmGUIglobals’
topTable.exons : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
topTable.exons : onOK: no visible binding for global variable
‘.affylmGUIglobals’
topTable.exons : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
topTable.exons : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
topTable.exons : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
topTable.exons: no visible binding for global variable ‘ReturnVal’
topTable.genes: no visible binding for global variable ‘res.genes’
topTable.genes: no visible binding for global variable
‘.affylmGUIglobals’
topTable.genes : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
topTable.genes : onOK: no visible binding for global variable
‘.affylmGUIglobals’
topTable.genes : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
topTable.genes : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
topTable.genes : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
topTable.genes: no visible binding for global variable ‘ReturnVal’
trainTest: no visible binding for global variable
‘affylmGUIenvironment’
trainTest: no visible binding for global variable ‘.affylmGUIglobals’
trainTest : onOK: no visible binding for global variable
‘.affylmGUIglobals’
trainTest : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
trainTest : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
trainTest: possible error in Try(x = exprs(testAffyData)): unused
argument (x = exprs(testAffyData))
trainTest: no visible global function definition for ‘pamr.train’
trainTest: no visible global function definition for ‘pamr.cv’
trainTest: no visible global function definition for ‘pamr.plotcv’
trainTest : onOK: no visible binding for global variable
‘affylmGUIenvironment’
trainTest: no visible global function definition for ‘pamr.plotcen’
trainTest: no visible global function definition for ‘pamr.confusion’
trainTest: no visible global function definition for ‘pamr.plotcvprob’
trainTest: no visible global function definition for ‘pamr.listgenes’
trainTest: no visible global function definition for ‘pdmClass’
trainTest: no visible global function definition for ‘pdmClass.cv’
trainTest: no visible global function definition for ‘confusion’
trainTest: no visible global function definition for ‘pdmGenes’
tuxedoMenu: no visible binding for global variable
‘affylmGUIenvironment’
tuxedoMenu: no visible binding for global variable ‘.affylmGUIglobals’
tuxedoSetup: no visible binding for global variable
‘affylmGUIenvironment’
updateLibs: no visible binding for global variable ‘.affylmGUIglobals’
updateLibs: no visible global function definition for
‘biocinstallRepos’
variantExons: no visible binding for global variable
‘.affylmGUIglobals’
variantExons: no visible global function definition for ‘matchMatrix’
variantSI: no visible binding for global variable ‘.affylmGUIglobals’
variantSI: no visible binding for global variable
‘affylmGUIenvironment’
variantSI: no visible binding for global variable ‘huex.variantexons’
variantSI: no visible binding for global variable ‘moex.variantexons’
variantSI: no visible binding for global variable ‘raex.variantexons’
VennDiagram: no visible binding for global variable ‘.affylmGUIglobals’
VennDiagram : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
VennDiagram : onOK: no visible binding for global variable
‘.affylmGUIglobals’
VennDiagram : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
VennDiagram: no visible binding for global variable
‘affylmGUIenvironment’
VennDiagram : plotFunction: no visible binding for global variable
‘include’
VennDiagram: no visible global function definition for ‘vennCounts’
whichKindOfArray: no visible binding for global variable
‘.affylmGUIglobals’
whichKindOfArray: no visible binding for global variable
‘affylmGUIenvironment’
whichKindOfArray: no visible binding for '<<-' assignment to
‘ReturnVal’
whichKindOfArray : onOK: no visible binding for '<<-' assignment to
‘ReturnVal’
whichKindOfArray : onOK: no visible binding for global variable
‘.affylmGUIglobals’
whichKindOfArray : onCancel: no visible binding for global variable
‘.affylmGUIglobals’
whichKindOfArray : <anonymous>: no visible binding for global variable
‘.affylmGUIglobals’
whichKindOfArray: no visible binding for global variable ‘ReturnVal’
wrapNGS: no visible binding for global variable ‘.affylmGUIglobals’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [26s/28s] OK
* checking PDF version of manual ... OK
* DONE
NOTE: There were 4 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/oneChannelGUI.Rcheck/00check.log’
for details.