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CHECK report for beadarraySNP on malbec2

This page was generated on 2019-10-16 11:56:11 -0400 (Wed, 16 Oct 2019).

Package 122/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarraySNP 1.50.0
Jan Oosting
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/beadarraySNP
Branch: RELEASE_3_9
Last Commit: 137a6b8
Last Changed Date: 2019-05-02 11:53:06 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarraySNP
Version: 1.50.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:beadarraySNP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings beadarraySNP_1.50.0.tar.gz
StartedAt: 2019-10-16 00:00:25 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:01:39 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 74.0 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:beadarraySNP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings beadarraySNP_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/beadarraySNP.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarraySNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘beadarraySNP’ version ‘1.50.0’
* 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 for sufficient/correct file permissions ... 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
* 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 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 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/beadarraySNP.Rcheck/00check.log’
for details.



Installation output

beadarraySNP.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL beadarraySNP
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘beadarraySNP’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (beadarraySNP)

Tests output


Example timings

beadarraySNP.Rcheck/beadarraySNP-Ex.timings

nameusersystemelapsed
GenomicReports2.6610.0282.699
PolarTransforms0.020.000.02
SnpSetSegments-class0.0020.0000.002
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes0.0070.0000.007
dist.GT0.0350.0000.035
heterozygosity0.0170.0000.017
heterozygousSNPs0.0480.0000.049
normalizeBetweenAlleles.SNP0.0360.0000.036
normalizeBetweenSubsamples.SNP0.0250.0000.025
normalizeLoci.SNP0.0200.0000.021
normalizeWithinArrays.SNP0.020.000.02
pdfChromosomesSmoothCopyNumber0.0000.0000.001
plotQC0.0030.0040.007
read.SnpSetIllumina0.5120.0001.026
removeLowQualitySamples0.0330.0000.033
reportSamplePanelQC-methods0.010.000.01
standardNormalization0.0860.0000.087