Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:05 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for beadarraySNP on nebbiolo2


To the developers/maintainers of the beadarraySNP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/beadarraySNP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 134/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarraySNP 1.60.0  (landing page)
Jan Oosting
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/beadarraySNP
git_branch: RELEASE_3_14
git_last_commit: baf3162
git_last_commit_date: 2021-10-26 11:50:17 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: beadarraySNP
Version: 1.60.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:beadarraySNP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings beadarraySNP_1.60.0.tar.gz
StartedAt: 2022-04-12 06:29:42 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:30:37 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 55.0 seconds
RetCode: 0
Status:   OK  
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:beadarraySNP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings beadarraySNP_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/beadarraySNP.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.60.0’
* 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 ‘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 ‘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 ‘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
  ‘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 ‘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
  ‘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
  ‘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
  ‘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’
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 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", "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-3.14-bioc/meat/beadarraySNP.Rcheck/00check.log’
for details.



Installation output

beadarraySNP.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL beadarraySNP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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
GenomicReports1.8370.0081.845
PolarTransforms0.0590.0000.058
SnpSetSegments-class0.0010.0000.001
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes0.0030.0000.004
dist.GT0.0810.0000.082
heterozygosity0.010.000.01
heterozygousSNPs0.0290.0000.028
normalizeBetweenAlleles.SNP0.0200.0000.019
normalizeBetweenSubsamples.SNP0.0080.0040.013
normalizeLoci.SNP0.0100.0000.009
normalizeWithinArrays.SNP0.0110.0000.011
pdfChromosomesSmoothCopyNumber000
plotQC0.0060.0000.005
read.SnpSetIllumina0.2570.0000.258
removeLowQualitySamples0.0180.0000.018
reportSamplePanelQC-methods0.0060.0000.006
standardNormalization0.0380.0000.038