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BioC 3.5: CHECK report for oneChannelGUI on veracruz2

This page was generated on 2017-10-18 14:28:12 -0400 (Wed, 18 Oct 2017).

Package 924/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oneChannelGUI 1.42.0
Raffaele A Calogero
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/oneChannelGUI
Branch: RELEASE_3_5
Last Commit: f5ce8f1
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: oneChannelGUI
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oneChannelGUI_1.42.0.tar.gz
StartedAt: 2017-10-18 06:54:52 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 07:00:55 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 363.0 seconds
RetCode: 0
Status:  OK 
CheckDir: oneChannelGUI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oneChannelGUI_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/oneChannelGUI.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oneChannelGUI/DESCRIPTION’ ... OK
* this is package ‘oneChannelGUI’ version ‘1.42.0’
* 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 ... 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’
.delta.plot1: no visible global function definition for ‘nobs’
.delta.plot1: no visible global function definition for ‘ecdf’
.delta.plot1: no visible global function definition for ‘axis’
.delta.plot1: no visible global function definition for ‘par’
.delta.plot1: no visible global function definition for ‘lines’
.delta.plot1: no visible global function definition for ‘text’
.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’
.length.stat: no visible global function definition for ‘pdf’
.length.stat: no visible global function definition for ‘legend’
.length.stat: no visible global function definition for ‘par’
.length.stat: no visible global function definition for ‘dev.off’
.mappingWgenominator: no visible binding for global variable
  ‘affylmGUIenvironment’
.mappingWgenominator: no visible global function definition for ‘runif’
.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’
.pamr.confusion.mod: no visible global function definition for
  ‘model.matrix’
.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 ‘predict’
.perm.pdmclass: no visible global function definition for ‘pdmClass.cv’
.perm.pdmclass: no visible global function definition for ‘confusion’
.plotDensity: no visible binding for global variable ‘density’
.plotDensity: no visible global function definition for ‘matplot’
.rawpCheckExons: no visible binding for global variable
  ‘affylmGUIenvironment’
.rawpCheckExons: no visible binding for global variable
  ‘.affylmGUIglobals’
.rawpCheckExons: no visible global function definition for ‘par’
.rawpCheckExons: no visible global function definition for ‘hist’
.reads2logos: no visible global function definition for ‘barplot’
.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 ‘organism’
.unionReads: no visible global function definition for ‘provider’
.unionReads: no visible global function definition for
  ‘providerVersion’
.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’
AptMidas: no visible global function definition for ‘hist’
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
  ‘model.matrix’
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: no visible global function definition for
  ‘estimateSizeFactors’
DESeqInterface: no visible global function definition for
  ‘estimateDispersions’
DESeqInterface : .plotDispEsts: no visible global function definition
  for ‘counts’
DESeqInterface : .plotDispEsts: no visible global function definition
  for ‘fitInfo’
DESeqInterface : .plotDispEsts: no visible global function definition
  for ‘lines’
DESeqInterface: no visible global function definition for ‘par’
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’
DESeqInterface : .plotDE: no visible global function definition for
  ‘points’
DESeqInterface : .plotDE: no visible global function definition for
  ‘abline’
EDANtFreq: no visible binding for global variable
  ‘affylmGUIenvironment’
EDANtFreq: no visible binding for global variable ‘.affylmGUIglobals’
EDANtFreq: no visible global function definition for ‘DataFrame’
EDANtFreq: no visible global function definition for
  ‘elementMetadata<-’
EDANtFreq: no visible global function definition for ‘elementMetadata’
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
  ‘elementMetadata’
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’
EDAbetweenLane: no visible global function definition for ‘par’
EDAbetweenLane: no visible global function definition for ‘boxplot’
EDAbiasPlot: no visible binding for global variable
  ‘affylmGUIenvironment’
EDAbiasPlot: no visible binding for global variable ‘.affylmGUIglobals’
EDAbiasPlot: no visible global function definition for
  ‘elementMetadata’
EDAbiasPlot: no visible global function definition for
  ‘newSeqExpressionSet’
EDAbiasPlot: no visible global function definition for ‘par’
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 ‘elementMetadata’
EDAboxplot: no visible global function definition for
  ‘newSeqExpressionSet’
EDAboxplot: no visible global function definition for ‘boxplot’
EDAplotQuality: no visible binding for global variable
  ‘affylmGUIenvironment’
EDAplotQuality: no visible binding for global variable
  ‘.affylmGUIglobals’
EDAplotQuality: no visible global function definition for ‘DataFrame’
EDAplotQuality: no visible global function definition for
  ‘elementMetadata<-’
EDAplotQuality: no visible global function definition for ‘plotQuality’
EDAplotQuality: no visible global function definition for ‘legend’
EDAplotQuality: no visible global function definition for
  ‘elementMetadata’
EDAplotQuality: no visible global function definition for ‘rainbow’
EDAreadNumber: no visible binding for global variable
  ‘affylmGUIenvironment’
EDAreadNumber: no visible binding for global variable
  ‘.affylmGUIglobals’
EDAreadNumber: no visible global function definition for ‘DataFrame’
EDAreadNumber: no visible global function definition for
  ‘elementMetadata<-’
EDAreadNumber: no visible global function definition for ‘barplot’
EDAreadNumber: no visible global function definition for
  ‘elementMetadata’
EDAreadNumber: no visible global function definition for ‘rainbow’
EDAwithinLane: no visible binding for global variable
  ‘affylmGUIenvironment’
EDAwithinLane: no visible binding for global variable
  ‘.affylmGUIglobals’
EDAwithinLane: no visible global function definition for
  ‘elementMetadata’
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 ‘par’
EDAwithinLane: no visible global function definition for ‘boxplot’
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 binding for global variable ‘GOBPPARENTS’
GOenrichment: no visible binding for global variable ‘GOMFPARENTS’
GOenrichment: no visible binding for global variable ‘GOCCPARENTS’
GOenrichment: no visible global function definition for ‘nodes’
GOenrichment: no visible global function definition for ‘makeNodeAttrs’
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’
OpenNgsfiles: no visible global function definition for ‘runif’
OpenmRNABam : onOK: no visible binding for global variable
  ‘affylmGUIenvironment’
OpenmRNABam: no visible binding for global variable
  ‘affylmGUIenvironment’
OpenmRNABam: no visible global function definition for ‘seqnames’
OpenmRNABam: no visible global function definition for ‘strand’
OpenmRNABam: no visible global function definition for
  ‘elementMetadata’
OpenmRNABam: no visible global function definition for
  ‘readGAlignments’
OpenmRNABam: no visible global function definition for ‘ngap’
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 global function definition for
  ‘par’
VennDiagram : plotFunction: no visible binding for global variable
  ‘include’
VennDiagram: no visible global function definition for ‘vennCounts’
VennDiagram: no visible global function definition for ‘plot.new’
adaptorTrimm: no visible binding for global variable
  ‘affylmGUIenvironment’
adaptorTrimm : onOK: no visible binding for global variable
  ‘affylmGUIenvironment’
adaptorTrimm: no visible global function definition for ‘pdf’
adaptorTrimm: no visible global function definition for ‘par’
adaptorTrimm: no visible global function definition for ‘hist’
adaptorTrimm: no visible global function definition for ‘dev.off’
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 global function definition for
  ‘par’
affyPlotMA : plotFunction: no visible binding for global variable
  ‘.affylmGUIglobals’
affyPlotMA : plotFunction: no visible global function definition for
  ‘title’
affyPlotMA: no visible global function definition for ‘plot.new’
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
  ‘makeCluster’
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
  ‘stopCluster’
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’
bayseqInterface: no visible global function definition for ‘par’
bayseqInterface: no visible global function definition for ‘hist’
bayseqInterface: no visible global function definition for ‘abline’
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’
biomartFilter: no visible global function definition for ‘par’
biomartFilter: no visible global function definition for ‘hist’
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’
cdsDiff: no visible global function definition for ‘points’
cdsDiff: no visible global function definition for ‘abline’
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’
closePdf: no visible global function definition for ‘dev.cur’
closePdf: no visible global function definition for ‘dev.off’
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’
crosshybFilter: no visible global function definition for ‘par’
crosshybFilter: no visible global function definition for ‘hist’
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’
dabgFilter: no visible global function definition for ‘par’
dabgFilter: no visible global function definition for ‘hist’
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
  ‘estimateSizeFactors’
desGenes: no visible global function definition for
  ‘estimateDispersions’
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’
deseq2Processing : .plotDE: no visible global function definition for
  ‘points’
deseq2Processing : .plotDE: no visible global function definition for
  ‘abline’
deseq2Processing: no visible global function definition for ‘par’
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’
dfMAplot: no visible global function definition for ‘par’
dfMAplot: no visible global function definition for ‘points’
dfMAplot: no visible global function definition for ‘abline’
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 ‘par’
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 ‘p.adjust’
edgerInterface: no visible global function definition for ‘topTags’
edgerInterface: no visible global function definition for ‘par’
edgerInterface: no visible global function definition for ‘hist’
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’
erankProdAltSpl: no visible global function definition for ‘par’
erankProdAltSpl: no visible global function definition for ‘hist’
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’
erankProdAltSplFilter: no visible global function definition for ‘par’
erankProdAltSplFilter: no visible global function definition for ‘hist’
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 ‘runif’
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
  ‘dbGetQuery’
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 ‘genes’
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’
geneDiff: no visible global function definition for ‘points’
geneDiff: no visible global function definition for ‘abline’
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.one.splice.index: no visible global function definition for
  ‘par’
inspecting.one.splice.index: no visible global function definition for
  ‘abline’
inspecting.one.splice.index: no visible global function definition for
  ‘legend’
inspecting.one.splice.index: no visible global function definition for
  ‘points’
inspecting.splice.index: no visible binding for global variable
  ‘.affylmGUIglobals’
inspecting.splice.index: no visible binding for global variable
  ‘affylmGUIenvironment’
inspecting.splice.index: no visible global function definition for
  ‘pdf’
inspecting.splice.index: no visible global function definition for
  ‘par’
inspecting.splice.index: no visible global function definition for
  ‘abline’
inspecting.splice.index: no visible global function definition for
  ‘legend’
inspecting.splice.index: no visible global function definition for
  ‘points’
inspecting.splice.index: no visible global function definition for
  ‘dev.off’
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’
intensityFilter: no visible global function definition for ‘par’
intensityFilter: no visible global function definition for ‘hist’
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: no visible global function definition for ‘legend’
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’
intronicBg: no visible global function definition for ‘abline’
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’
iqrFilter: no visible global function definition for ‘par’
iqrFilter: no visible global function definition for ‘hist’
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’
isoDiff: no visible global function definition for ‘points’
isoDiff: no visible global function definition for ‘abline’
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: no visible global function definition for ‘hist’
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 ‘model.matrix’
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 ‘par’
mRNAmiRCor: no visible global function definition for ‘hist’
mRNAmiRCor: no visible global function definition for ‘pdf’
mRNAmiRCor: no visible global function definition for ‘PlotGroups’
mRNAmiRCor: no visible global function definition for ‘dev.off’
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 global function definition for
  ‘elementMetadata’
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 ‘genome<-’
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’
makeGeneScaffold: no visible global function definition for ‘GRanges’
makeGeneScaffold: no visible global function definition for ‘Rle’
makeGeneScaffold: no visible global function definition for
  ‘elementMetadata’
mapping2RefSeq: no visible binding for global variable
  ‘.affylmGUIglobals’
mapping2RefSeq: no visible binding for global variable
  ‘affylmGUIenvironment’
mapping2RefSeq: no visible global function definition for ‘runif’
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 ‘runif’
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 ‘runif’
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 global function definition for
  ‘par’
masigpro.view : plotFunction: no visible binding for global variable
  ‘include’
masigpro.view: no visible global function definition for ‘vennCounts’
masigpro.view: no visible global function definition for ‘plot.new’
masigpro.view : onOK: no visible binding for global variable
  ‘affylmGUIenvironment’
masigpro.view: no visible global function definition for ‘pdf’
masigpro.view: no visible global function definition for ‘PlotGroups’
masigpro.view: no visible global function definition for ‘dev.off’
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’
metaArrayIC: no visible global function definition for ‘hist’
metaArrayIC: no visible global function definition for ‘par’
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’
mirnaTable: no visible global function definition for ‘reshape’
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’
normBoxplot: no visible global function definition for ‘boxplot’
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 : plotHist: no visible global function definition for
  ‘legend’
ocPlotHist : plotHist: no visible global function definition for ‘par’
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 : plotPCA: no visible global function definition for ‘prcomp’
ocPlotPCA : plotPCA: no visible global function definition for ‘hclust’
ocPlotPCA : plotPCA: no visible global function definition for ‘dist’
ocPlotPCA : plotPCA: no visible global function definition for ‘par’
ocPlotPCA : plotPCA: no visible global function definition for ‘text’
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 global function definition for ‘dev.cur’
openPdf: no visible global function definition for ‘dev.off’
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’
openPdf: no visible global function definition for ‘pdf’
permuting: no visible global function definition for ‘phyper’
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 binding for global variable ‘GOBPPARENTS’
plotGO: no visible global function definition for ‘nodes’
plotGO: no visible global function definition for ‘removeNode’
plotGO: no visible global function definition for ‘getGOTerm’
plotGO: no visible binding for global variable ‘GOMFPARENTS’
plotGO: no visible binding for global variable ‘GOCCPARENTS’
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’
rawBoxplotPN: no visible global function definition for ‘par’
rawBoxplotPN: no visible global function definition for ‘boxplot’
rawpCheck: no visible binding for global variable
  ‘affylmGUIenvironment’
rawpCheck: no visible binding for global variable ‘.affylmGUIglobals’
rawpCheck: no visible global function definition for ‘par’
rawpCheck: no visible global function definition for ‘hist’
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’
refiningPeaks: no visible global function definition for ‘abline’
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
  ‘dbGetQuery’
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’
retrievePSRseq: no visible global function definition for ‘runif’
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’
retrievePSRseq1gid: no visible global function definition for ‘runif’
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’
reviqrFilter: no visible global function definition for ‘par’
reviqrFilter: no visible global function definition for ‘hist’
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
  ‘pnorm’
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 ‘par’
sample.size.evaluation: no visible global function definition for
  ‘legend’
sample.size.evaluation: no visible global function definition for
  ‘nobs’
sample.size.evaluation: no visible global function definition for
  ‘title’
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: no visible global function definition for ‘par’
trainTest: no visible global function definition for ‘prcomp’
trainTest: no visible global function definition for ‘hclust’
trainTest: no visible global function definition for ‘dist’
trainTest: no visible global function definition for ‘text’
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 ‘predict’
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’
wrapperMirnaCounts: no visible global function definition for ‘assay’
wrapperMirnaCounts: no visible global function definition for ‘pdf’
wrapperMirnaCounts: no visible global function definition for
  ‘plotDispEsts’
wrapperMirnaCounts: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  .affylmGUIglobals .bowtieGenomes Abort CDS DESeq
  DESeqDataSetFromMatrix DGEList DataFrame DisplayPars GOBPPARENTS
  GOCCPARENTS GOGraph GOMFPARENTS GRanges GRangesForUCSCGenome
  GenomeData GenomicData Hsapiens KEGGEXTID2PATHID KEGGPATHID2NAME
  Mmusculus MulticoreParam NetAffxResource PlotGroups RP RPadvance
  ReadAffy ReturnAnn ReturnFilter ReturnNetaffx ReturnVal ReturnValX
  Rle RmiR.Hs.miRNA_dbconn Rnorvegicus T.fit aaf.handler aafTableAnn
  abline affxAnnotation affxDescription affylmGUIenvironment
  aggregateExpData all.counts annlib annotatePeakInBatch assay axis
  barplot betweenLaneNormalization biasPlot biocinstallRepos
  biocparallel bowtie bowtieVal bowtie_build boxplot bplapply
  browserSession browserView calcNormFactors cdfName chrLength
  conditional<- confusion contrasts.fit counts crosshybraex.annotation
  dbGetQuery delta density dev.cur dev.off diffData dist
  duplicateCorrelation eBayes ecdf elementMetadata elementMetadata<-
  estimateCommonDisp estimateDispersions estimateSizeFactors
  estimateTagwiseDisp exactTest expresso extendReads fcpVal filterfun
  filtermirnapath fitInfo fpkm gcrma gdPlot gdapply geneIds genefilter
  genes genome<- geoVSbioc get.siggenes getAnnotation getBM getDataEnv
  getGOTerm getGenes getLikelihoods.NB getPriorN getPriors.NB getSYMBOL
  getSequence getTable getTargetsFromSource glibVal goseq gunzip
  hairpin hclust hist hs.path.name huex.annotation huex.variantexons
  hyperGTest importToExpData include intcor isoforms jetta.do.mads
  jetta.read.expression jetta.read.mads.output legend limmaExon lines
  lm.series lmFit loadmirnapathways loadmirnatogene lookUp
  make.design.matrix makeCluster makeGene makeNodeAttrs
  makeRectangleOverlay makeTranscript matchMatrix matplot mature.GA
  mergeExprs model.matrix moex.annotation moex.variantexons
  mt.rawp2adjp mt.teststat my.fset nbinomTest newCountDataSet
  newCountDataSetFromHTSeqCount newSeqExpressionSet ngap nobs nodes
  normalize.loess normalize.qspline normalize.quantiles nullp organism
  p.adjust p.vector pOverA pamr.confusion pamr.cv pamr.listgenes
  pamr.plotcen pamr.plotcv pamr.plotcvprob pamr.train par pdf pdmClass
  pdmClass.cv pdmGenes phyper plot.new plotDEXSeq plotDensity
  plotDispEsts plotMDS.DGEList plotMDS.dge plotNtFrequency plotQuality
  plotSmear pnorm points power.randomized prcomp predict provider
  providerVersion pvalues raex.annotation raex.variantexons rainbow
  raw.fusions read.DNAStringSet read.mir read.phenoData readAnnotation
  readCufflinks readFASTA readGAlignments removeNode res.exons
  res.genes reshape results rlog rma runif sampleSize.randomized
  saveHTML seqnames ssize ssize.plot stopCluster strand
  summarizeByAnnotation tableName<- text title tmp tmpIR topCounts
  topGene topTags toptable track<- tt ucscTableQuery universeCounts
  universeMappedCount useDataset useMart vennCounts which.is.max
  withinLaneNormalization writeFASTA x x.exon
Consider adding
  importFrom("grDevices", "dev.cur", "dev.off", "pdf", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot", "hist",
             "legend", "lines", "matplot", "par", "plot.new", "points",
             "text", "title")
  importFrom("stats", "density", "dist", "ecdf", "hclust",
             "model.matrix", "nobs", "p.adjust", "phyper", "pnorm",
             "prcomp", "predict", "reshape", "runif")
to your NAMESPACE file.
* 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 ... 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-3.5-bioc/meat/oneChannelGUI.Rcheck/00check.log’
for details.


oneChannelGUI.Rcheck/00install.out:

* installing *source* package ‘oneChannelGUI’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oneChannelGUI)

oneChannelGUI.Rcheck/oneChannelGUI-Ex.timings:

nameusersystemelapsed
oneChannelGUI-package0.0010.0000.001
oneChannelGUI0.0010.0000.002