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) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:40 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (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 | ||||
|
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. |
| Package 134/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beadarraySNP 1.60.0 (landing page) Jan Oosting
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: beadarraySNP |
| Version: 1.60.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:beadarraySNP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings beadarraySNP_1.60.0.tar.gz |
| StartedAt: 2022-04-12 10:40:29 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 10:42:19 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 110.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: beadarraySNP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:beadarraySNP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings beadarraySNP_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/beadarraySNP.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 sizes of PDF files under ‘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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.14-bioc/meat/beadarraySNP.Rcheck/00check.log’
for details.
beadarraySNP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL beadarraySNP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)
beadarraySNP.Rcheck/beadarraySNP-Ex.timings
| name | user | system | elapsed | |
| GenomicReports | 2.903 | 0.170 | 3.278 | |
| PolarTransforms | 0.056 | 0.010 | 0.066 | |
| SnpSetSegments-class | 0.001 | 0.000 | 0.002 | |
| backgroundCorrect.SNP | 0.000 | 0.000 | 0.001 | |
| calculateQCarray | 0.000 | 0.001 | 0.000 | |
| compareGenotypes | 0.006 | 0.003 | 0.009 | |
| dist.GT | 0.142 | 0.008 | 0.152 | |
| heterozygosity | 0.018 | 0.004 | 0.022 | |
| heterozygousSNPs | 0.056 | 0.004 | 0.060 | |
| normalizeBetweenAlleles.SNP | 0.037 | 0.004 | 0.042 | |
| normalizeBetweenSubsamples.SNP | 0.029 | 0.003 | 0.032 | |
| normalizeLoci.SNP | 0.026 | 0.002 | 0.028 | |
| normalizeWithinArrays.SNP | 0.025 | 0.003 | 0.028 | |
| pdfChromosomesSmoothCopyNumber | 0.001 | 0.000 | 0.000 | |
| plotQC | 0.009 | 0.003 | 0.012 | |
| read.SnpSetIllumina | 0.773 | 0.020 | 0.796 | |
| removeLowQualitySamples | 0.034 | 0.003 | 0.037 | |
| reportSamplePanelQC-methods | 0.011 | 0.004 | 0.015 | |
| standardNormalization | 0.091 | 0.020 | 0.178 | |