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BioC 3.3: CHECK report for beadarraySNP on moscato2

This page was generated on 2016-10-13 12:47:54 -0700 (Thu, 13 Oct 2016).

Package 85/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarraySNP 1.38.0
Jan Oosting
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/beadarraySNP
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarraySNP
Version: 1.38.0
Command: rm -rf beadarraySNP.buildbin-libdir beadarraySNP.Rcheck && mkdir beadarraySNP.buildbin-libdir beadarraySNP.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarraySNP.buildbin-libdir beadarraySNP_1.38.0.tar.gz >beadarraySNP.Rcheck\00install.out 2>&1 && cp beadarraySNP.Rcheck\00install.out beadarraySNP-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=beadarraySNP.buildbin-libdir --install="check:beadarraySNP-install.out" --force-multiarch --no-vignettes --timings beadarraySNP_1.38.0.tar.gz
StartedAt: 2016-10-13 01:17:48 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:20:01 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 132.9 seconds
RetCode: 0
Status:  OK  
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf beadarraySNP.buildbin-libdir beadarraySNP.Rcheck && mkdir beadarraySNP.buildbin-libdir beadarraySNP.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarraySNP.buildbin-libdir beadarraySNP_1.38.0.tar.gz >beadarraySNP.Rcheck\00install.out 2>&1 && cp beadarraySNP.Rcheck\00install.out beadarraySNP-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=beadarraySNP.buildbin-libdir --install="check:beadarraySNP-install.out" --force-multiarch --no-vignettes --timings beadarraySNP_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/beadarraySNP.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarraySNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'beadarraySNP' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 whether package 'beadarraySNP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'DNAcopy' 'aCGH' 'affy' 'beadarray' 'limma' 'snapCGH'
  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
IlluminaGetGencalls: no visible global function definition for
  'read.table'
IlluminaGetOPAinfo: no visible global function definition for
  'read.table'
Sample_Map2Samplesheet: no visible global function definition for
  'read.table'
Sample_Map2Samplesheet: no visible global function definition for
  'write.table'
backgroundCorrect.SNP : delta.vec: no visible global function
  definition for 'quantile'
backgroundCorrect.SNP: no visible global function definition for
  'normexp.fit'
backgroundCorrect.SNP: no visible global function definition for
  'normexp.signal'
backgroundCorrect.SNP: no visible binding for global variable
  'bg.adjust'
backgroundEstimate : intminBG: no visible global function definition
  for 'lm'
backgroundEstimate: no visible global function definition for 'density'
calculateLair: no visible global function definition for 'quantile'
calculateQCarray: no visible global function definition for 'median'
convert2aCGH: no visible global function definition for 'create.aCGH'
createCNSummary: no visible global function definition for 'aggregate'
dist.GT: no visible global function definition for 'as.dist'
heterozygousSNPs: no visible binding for global variable 'quantile'
interactiveCNselect: no visible global function definition for
  'locator'
interactiveCNselect: no visible global function definition for 'text'
normalizeBetweenAlleles.SNP: no visible global function definition for
  'normalizeQuantiles'
normalizeBetweenSubsamples.SNP: no visible global function definition
  for 'normalizeQuantiles'
normalizeLoci.SNP: no visible binding for global variable 'median'
normalizeLoci.SNP: no visible global function definition for 'coef'
normalizeLoci.SNP: no visible global function definition for 'lm'
normalizeWithinArrays.SNP: no visible global function definition for
  'quantile'
pdfChromosomeGainLossLOH: no visible global function definition for
  'pdf'
pdfChromosomeGainLossLOH: no visible global function definition for
  'par'
pdfChromosomeGainLossLOH: no visible global function definition for
  'dev.off'
pdfChromosomesSmoothCopyNumber: no visible global function definition
  for 'pdf'
pdfChromosomesSmoothCopyNumber: no visible global function definition
  for 'par'
pdfChromosomesSmoothCopyNumber: no visible global function definition
  for 'dev.off'
pdfQC : reportSingleObject: no visible global function definition for
  'par'
pdfQC : reportSingleObject: no visible global function definition for
  'mtext'
pdfQC: no visible global function definition for 'pdf'
pdfQC: no visible global function definition for 'dev.off'
pdfSamplesSmoothCopyNumber: no visible global function definition for
  'pdf'
pdfSamplesSmoothCopyNumber: no visible global function definition for
  'dev.off'
plotGenomePanels: no visible global function definition for 'par'
plotGenomePanels: no visible global function definition for 'plot'
plotGenomePanels: no visible global function definition for 'abline'
plotGenomePanels: no visible global function definition for 'points'
plotGenomePanels: no visible global function definition for 'text'
plotGenomePanels: no visible global function definition for 'axis'
plotGenomePanels: no visible global function definition for 'segments'
plotGenomePanels: no visible global function definition for 'rect'
plotGoldenGate4OPA: no visible global function definition for 'par'
plotGoldenGate4OPA: no visible global function definition for 'plot'
plotGoldenGate4OPA: no visible global function definition for 'abline'
plotGoldenGate4OPA: no visible global function definition for 'points'
plotGoldenGate4OPA: no visible global function definition for 'text'
plotGoldenGate4OPA: no visible global function definition for 'axis'
plotGoldenGate4OPA: no visible global function definition for
  'segments'
plotGoldenGate4OPA: no visible global function definition for 'rect'
plotGroupZygosity: no visible global function definition for 'plot'
plotGroupZygosity: no visible global function definition for 'points'
read.SnpSetIllumina: no visible global function definition for
  'read.table'
read.SnpSetIllumina: no visible global function definition for
  'readIllumina'
read.SnpSetIllumina: no visible global function definition for
  'summarize'
read.SnpSetIllumina: no visible global function definition for
  'aggregate'
read.SnpSetIllumina: no visible binding for global variable 'median'
read.SnpSetIllumina: no visible binding for global variable 'sd'
read.SnpSetIllumina: no visible global function definition for
  'type.convert'
readReportfile: no visible global function definition for 'read.table'
removeLowQualityProbes: no visible global function definition for
  'median'
removeLowQualityProbes: no visible binding for global variable 'median'
removeLowQualitySamples: no visible binding for global variable
  'median'
reportChromosomeGainLossLOH: no visible global function definition for
  'plot'
reportChromosomeGainLossLOH: no visible global function definition for
  'par'
reportChromosomeGainLossLOH: no visible global function definition for
  'rect'
reportChromosomeGainLossLOH: no visible global function definition for
  'axis'
reportChromosomeGainLossLOH: no visible global function definition for
  'abline'
reportChromosomesSmoothCopyNumber: no visible global function
  definition for 'par'
reportChromosomesSmoothCopyNumber: no visible global function
  definition for 'plot'
reportChromosomesSmoothCopyNumber: no visible global function
  definition for 'legend'
reportChromosomesSmoothCopyNumber: no visible global function
  definition for 'abline'
reportChromosomesSmoothCopyNumber: no visible global function
  definition for 'rect'
reportChromosomesSmoothCopyNumber: no visible global function
  definition for 'points'
reportChromosomesSmoothCopyNumber: no visible global function
  definition for 'lines'
reportGenomeGainLossLOH: no visible global function definition for
  'plot'
reportGenomeGainLossLOH: no visible global function definition for
  'par'
reportGenomeGainLossLOH: no visible global function definition for
  'rect'
reportGenomeGainLossLOH: no visible global function definition for
  'abline'
reportGenomeGainLossLOH: no visible global function definition for
  'axis'
reportGenomeIntensityPlot: no visible global function definition for
  'aggregate'
reportGenomeIntensityPlot: no visible global function definition for
  'plot'
reportGenomeIntensityPlot: no visible global function definition for
  'par'
reportGenomeIntensityPlot: no visible global function definition for
  'abline'
reportGenomeIntensityPlot: no visible global function definition for
  'axis'
reportGenomeIntensityPlot: no visible global function definition for
  'points'
reportGenomeIntensityPlot: no visible global function definition for
  'segments'
reportGenomeIntensityPlot: no visible global function definition for
  'lines'
reportGenotypeSegmentation: no visible global function definition for
  'par'
reportGenotypeSegmentation: no visible global function definition for
  'plot'
reportGenotypeSegmentation: no visible global function definition for
  'points'
reportGenotypeSegmentation: no visible global function definition for
  'axis'
reportGenotypeSegmentation: no visible global function definition for
  'abline'
reportGenotypeSegmentation: no visible global function definition for
  'segments'
reportGroupZygosity: no visible global function definition for 'pdf'
reportGroupZygosity: no visible global function definition for 'par'
reportGroupZygosity: no visible global function definition for
  'dev.off'
reportSamplesSmoothCopyNumber: no visible global function definition
  for 'par'
reportSamplesSmoothCopyNumber: no visible global function definition
  for 'lines'
reportSamplesSmoothCopyNumber: no visible global function definition
  for 'rect'
reportSamplesSmoothCopyNumber: no visible global function definition
  for 'points'
reportSamplesSmoothCopyNumber: no visible global function definition
  for 'legend'
segmentate: no visible global function definition for 'smooth.CNA'
segmentate: no visible global function definition for 'CNA'
segmentate: no visible global function definition for 'aggregate'
segmentate.old: no visible global function definition for 'runDNAcopy'
segmentate.old: no visible global function definition for 'runHomHMM'
segmentate.old: no visible global function definition for 'runBioHMM'
segmentate.old: no visible global function definition for 'runGLAD'
segmentate.old: no visible global function definition for 'mergeStates'
plotQC,QCIllumina : image.plate: no visible global function definition
  for 'gray'
plotQC,QCIllumina : image.plate: no visible global function definition
  for 'image'
plotQC,QCIllumina : checkerboard: no visible global function definition
  for 'strwidth'
plotQC,QCIllumina : checkerboard: no visible global function definition
  for 'text'
plotQC,QCIllumina: no visible global function definition for 'rgb'
reportSamplePanelQC,QCIllumina: no visible global function definition
  for 'rgb'
reportSamplePanelQC,QCIllumina: no visible global function definition
  for 'barplot'
reportSamplePanelQC,QCIllumina: no visible global function definition
  for 'plot'
Undefined global functions or variables:
  CNA abline aggregate as.dist axis barplot bg.adjust coef create.aCGH
  density dev.off gray image legend lines lm locator median mergeStates
  mtext normalizeQuantiles normexp.fit normexp.signal par pdf plot
  points quantile read.table readIllumina rect rgb runBioHMM runDNAcopy
  runGLAD runHomHMM sd segments smooth.CNA strwidth summarize text
  type.convert write.table
Consider adding
  importFrom("grDevices", "dev.off", "gray", "pdf", "rgb")
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "locator", "mtext", "par", "plot", "points",
             "rect", "segments", "strwidth", "text")
  importFrom("stats", "aggregate", "as.dist", "coef", "density", "lm",
             "median", "quantile", "sd")
  importFrom("utils", "read.table", "type.convert", "write.table")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/beadarraySNP.Rcheck/00check.log'
for details.


beadarraySNP.Rcheck/00install.out:


install for i386

* installing *source* package 'beadarraySNP' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'beadarraySNP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beadarraySNP' as beadarraySNP_1.38.0.zip
* DONE (beadarraySNP)

beadarraySNP.Rcheck/examples_i386/beadarraySNP-Ex.timings:

nameusersystemelapsed
GenomicReports3.400.053.98
PolarTransforms0.030.010.05
SnpSetSegments-class0.020.000.01
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes0.000.020.02
dist.GT0.060.000.06
heterozygosity0.030.000.03
heterozygousSNPs0.050.010.06
normalizeBetweenAlleles.SNP0.050.000.05
normalizeBetweenSubsamples.SNP0.010.000.01
normalizeLoci.SNP0.020.020.04
normalizeWithinArrays.SNP0.010.000.01
pdfChromosomesSmoothCopyNumber000
plotQC0.020.000.02
read.SnpSetIllumina2.140.002.13
removeLowQualitySamples0.040.000.05
reportSamplePanelQC-methods0.020.000.02
standardNormalization0.080.010.09

beadarraySNP.Rcheck/examples_x64/beadarraySNP-Ex.timings:

nameusersystemelapsed
GenomicReports3.210.054.40
PolarTransforms0.030.000.03
SnpSetSegments-class000
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes0.020.000.02
dist.GT0.050.000.04
heterozygosity0.030.000.04
heterozygousSNPs0.060.000.06
normalizeBetweenAlleles.SNP0.050.000.04
normalizeBetweenSubsamples.SNP0.030.000.04
normalizeLoci.SNP0.030.020.04
normalizeWithinArrays.SNP0.030.000.03
pdfChromosomesSmoothCopyNumber000
plotQC0.000.010.02
read.SnpSetIllumina1.970.021.98
removeLowQualitySamples0.040.000.05
reportSamplePanelQC-methods0.020.000.01
standardNormalization0.080.000.08