BioC 3.1: CHECK report for oneChannelGUI on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oneChannelGUI_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/oneChannelGUI.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oneChannelGUI/DESCRIPTION’ ... OK
* this is package ‘oneChannelGUI’ version ‘1.34.0’
* 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 ... [32s/35s] OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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:
  ‘BSgenome.Hsapiens.UCSC.hg19’ ‘BSgenome.Mmusculus.UCSC.mm9’
  ‘BSgenome.Rnorvegicus.UCSC.rn4’ ‘Genominator’ ‘affy’ ‘affyPLM’
  ‘chipseq’ ‘maSigPro’
  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'
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'
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'
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'
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'
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'
ML.edesign: warning in get("NormalizedAffyData", 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'
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'
VennDiagram: warning in mget(mySel[, 1], env = getDataEnv("ENTREZID",
  lib), ifnotfound = NA): 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'
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'
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'
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'
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'
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'
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'
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'
mRNAbowtieRun: warning in get("Threads", 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'
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'
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'
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'
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'
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'
.GetContrasts: no visible binding for global variable
  ‘affylmGUIenvironment’
.GetContrasts: no visible global function definition for ‘limmaExon’
.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’
.countMature : .extractMatureCounts: no visible global function
  definition for ‘readGAlignments’
.countMature: no visible binding for global variable ‘mature.GA’
.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’
.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’
.matureOnHairpin: no visible global function definition for
  ‘bowtie_build’
.matureOnHairpin: no visible global function definition for ‘bowtie’
.matureOnHairpin: no visible global function definition for
  ‘readGAlignments’
.openmiRNAFile: no visible binding for global variable
  ‘.affylmGUIglobals’
.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’
.trim: no visible global function definition for ‘MulticoreParam’
.trim: no visible global function definition for ‘bplapply’
.unionReads: no visible global function definition for ‘GenomeData’
.unionReads: no visible global function definition for ‘gdapply’
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’
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’
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’
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’
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’
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’
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’
ExportNormalizedExpressionValues: no visible binding for global
  variable ‘affylmGUIenvironment’
ExportNormalizedExpressionValues1: no visible binding for global
  variable ‘.affylmGUIglobals’
ExportNormalizedExpressionValues1: no visible binding for global
  variable ‘affylmGUIenvironment’
ExportfeatureNames: no visible binding for global variable
  ‘.affylmGUIglobals’
ExportfeatureNames: no visible binding for global variable
  ‘affylmGUIenvironment’
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 global function definition for ‘nodes’
GOenrichment: no visible global function definition for ‘makeNodeAttrs’
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’
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’
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’
NGSreformat: no visible binding for global variable
  ‘affylmGUIenvironment’
NGSreformat : onOK: no visible binding for global variable
  ‘affylmGUIenvironment’
NewLimmaFile: no visible binding for global variable
  ‘affylmGUIenvironment’
NewLimmaFileNGS: 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’
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’
OpenNgsfiles : onOK: no visible binding for global variable
  ‘affylmGUIenvironment’
OpenNgsfiles: 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
  ‘readGAlignments’
OpenmRNABam: no visible global function definition for ‘matchMatrix’
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’
OpenmiRanalyserfiles : onOK: no visible binding for global variable
  ‘affylmGUIenvironment’
OpenmiRanalyserfiles: no visible binding for global variable
  ‘affylmGUIenvironment’
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’
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’
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’
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’
SetED: no visible binding for global variable ‘.affylmGUIglobals’
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’
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’
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’
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’
desGenes: no visible global function definition for
  ‘newCountDataSetFromHTSeqCount’
desGenes: no visible global function definition for ‘nbinomTest’
deseq2Processing: no visible binding for global variable
  ‘.affylmGUIglobals’
deseq2Processing : onOK: no visible binding for '<<-' assignment to
  ‘fcpVal’
deseq2Processing : onOK: no visible binding for global variable
  ‘.affylmGUIglobals’
deseq2Processing : onCancel: no visible binding for '<<-' assignment to
  ‘fcpVal’
deseq2Processing : onCancel: no visible binding for global variable
  ‘.affylmGUIglobals’
deseq2Processing : <anonymous>: no visible binding for global variable
  ‘.affylmGUIglobals’
deseq2Processing: no visible binding for global variable ‘fcpVal’
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’
downloadShrimp: no visible binding for '<<-' assignment to ‘Abort’
downloadShrimp: no visible binding for global variable
  ‘affylmGUIenvironment’
downloadShrimp: no visible binding for global variable
  ‘.affylmGUIglobals’
downloadShrimp : onCancel: no visible binding for global variable
  ‘.affylmGUIglobals’
downloadShrimp : onCancel: no visible binding for '<<-' assignment to
  ‘Abort’
downloadShrimp : onOK: no visible binding for global variable
  ‘.affylmGUIglobals’
downloadShrimp : <anonymous>: no visible binding for global variable
  ‘.affylmGUIglobals’
downloadShrimp: no visible binding for global variable ‘Abort’
eSet4meV: no visible binding for global variable ‘affylmGUIenvironment’
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’
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’
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’
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’
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’
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’
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’
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’
filteringTable: no visible binding for global variable
  ‘.affylmGUIglobals’
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’
fusionNS: no visible binding for global variable ‘.affylmGUIglobals’
fusionNS: no visible binding for global variable ‘raw.fusions’
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’
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’
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’
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’
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")
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’
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’
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’
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’
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’
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’
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’
miRNAde: no visible binding for global variable ‘.affylmGUIglobals’
miRNAde : <anonymous>: no visible binding for global variable
  ‘.affylmGUIglobals’
miRNAde: no visible binding for '<<-' assignment to ‘biocparallel’
miRNAde: no visible binding for global variable ‘biocparallel’
miRNAde: no visible binding for global variable ‘all.counts’
miRNAde: no visible binding for global variable ‘affylmGUIenvironment’
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’
mirPath: no visible binding for global variable ‘.affylmGUIglobals’
mirPath : <anonymous>: no visible global function definition for
  ‘getTargetsFromSource’
mirPath : onCancel: no visible binding for global variable
  ‘.affylmGUIglobals’
mirPath : onOK: no visible binding for global variable
  ‘.affylmGUIglobals’
mirPath : <anonymous>: no visible binding for global variable
  ‘.affylmGUIglobals’
mirPath : onOK: no visible binding for '<<-' assignment to ‘fcpVal’
mirPath : onCancel: no visible binding for '<<-' assignment to ‘fcpVal’
mirPath: no visible binding for global variable ‘fcpVal’
mirPath: no visible global function definition for ‘filtermirnapath’
mirPath: no visible global function definition for ‘loadmirnatogene’
mirPath: no visible binding for global variable ‘KEGGEXTID2PATHID’
mirPath: no visible binding for global variable ‘KEGGPATHID2NAME’
mirPath: no visible global function definition for ‘loadmirnapathways’
mirnaTable: no visible binding for global variable ‘hs.path.name’
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’
ngsperlDownload: no visible binding for global variable
  ‘.affylmGUIglobals’
ngsperlDownload: no visible binding for global variable
  ‘affylmGUIenvironment’
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’
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’
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 global function definition for ‘nodes’
plotGO: no visible global function definition for ‘removeNode’
plotGO: no visible global function definition for ‘getGOTerm’
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’
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’
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’
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’
rankingConversion: no visible binding for global variable
  ‘affylmGUIenvironment’
rankingConversion: no visible binding for global variable
  ‘.affylmGUIglobals’
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’
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’
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’
setBinDir: no visible binding for global variable ‘.affylmGUIglobals’
setBinDir: no visible binding for global variable
  ‘affylmGUIenvironment’
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’
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’
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’
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’
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’
wrapperMirnaCounts: no visible binding for global variable
  ‘affylmGUIenvironment’
wrapperMirnaCounts: no visible global function definition for
  ‘MulticoreParam’
wrapperMirnaCounts: no visible global function definition for
  ‘bplapply’
wrapperMirnaCounts: no visible global function definition for
  ‘DESeqDataSetFromMatrix’
wrapperMirnaCounts: no visible global function definition for ‘DESeq’
wrapperMirnaCounts: no visible global function definition for ‘results’
wrapperMirnaCounts: no visible global function definition for ‘rlog’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/23s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/oneChannelGUI.Rcheck/00check.log’
for details.
name	user	system	elapsed
oneChannelGUI-package	0.000	0.000	0.001
oneChannelGUI	0.001	0.000	0.001
BioC 3.1: CHECK report for oneChannelGUI on morelia

Summary

Command output
