Gro Nilsen
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/copynumber |
| Branch: RELEASE_3_9 |
| Last Commit: b55dbdb |
| Last Changed Date: 2019-05-02 11:53:42 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:51:19 -0400 (Wed, 16 Oct 2019).
| Package 343/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| copynumber 1.24.0 Gro Nilsen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: copynumber |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:copynumber.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings copynumber_1.24.0.tar.gz |
| StartedAt: 2019-10-16 01:46:54 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:50:12 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 197.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: copynumber.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:copynumber.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings copynumber_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/copynumber.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copynumber/DESCRIPTION’ ... OK
* this is package ‘copynumber’ version ‘1.24.0’
* 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 ‘copynumber’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: ‘BiocGenerics’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addArmlines: no visible global function definition for ‘modifyList’
addArmlines: no visible global function definition for ‘abline’
addChromlines: no visible global function definition for ‘modifyList’
addChromlines: no visible global function definition for ‘abline’
addChromlines: no visible global function definition for ‘mtext’
addToFreqPlot: no visible global function definition for ‘abline’
addToFreqPlot: no visible global function definition for ‘axis’
addToFreqPlot: no visible global function definition for ‘title’
addToPlot: no visible global function definition for ‘axis’
addToPlot: no visible global function definition for ‘mtext’
addToPlot: no visible global function definition for ‘title’
addToPlot: no visible global function definition for ‘abline’
aspcf: no visible global function definition for ‘read.table’
aspcf: no visible global function definition for ‘write.table’
c.lines: no visible global function definition for ‘lines’
chromPattern: no visible global function definition for ‘rect’
chromPattern: no visible global function definition for ‘par’
chromosomeAberration: no visible global function definition for
‘dev.cur’
chromosomeAberration: no visible global function definition for
‘dev.new’
chromosomeAberration: no visible global function definition for ‘par’
chromosomeAberration: no visible global function definition for ‘plot’
chromosomeAberration: no visible global function definition for ‘rect’
chromosomeAberration: no visible global function definition for ‘title’
chromosomeAberration: no visible global function definition for ‘axis’
chromosomeAberration: no visible global function definition for
‘abline’
chromosomeAberration: no visible global function definition for
‘devAskNewPage’
chromosomeFreq: no visible global function definition for ‘dev.cur’
chromosomeFreq: no visible global function definition for ‘dev.new’
chromosomeFreq: no visible global function definition for ‘par’
chromosomeFreq: no visible global function definition for ‘plot’
chromosomeFreq: no visible global function definition for ‘rect’
chromosomeFreq: no visible global function definition for ‘abline’
chromosomeFreq: no visible global function definition for ‘title’
chromosomeFreq: no visible global function definition for
‘devAskNewPage’
chromosomeHeat: no visible global function definition for ‘dev.cur’
chromosomeHeat: no visible global function definition for ‘dev.new’
chromosomeHeat: no visible global function definition for ‘par’
chromosomeHeat: no visible global function definition for ‘plot’
chromosomeHeat: no visible global function definition for ‘rect’
chromosomeHeat: no visible global function definition for ‘title’
chromosomeHeat: no visible global function definition for ‘axis’
chromosomeHeat: no visible global function definition for ‘abline’
chromosomeHeat: no visible global function definition for
‘devAskNewPage’
colorSetup: no visible global function definition for
‘colorRampPalette’
connectSeg: no visible global function definition for ‘segments’
draw.roundEdge: no visible global function definition for ‘polygon’
drawStalk: no visible global function definition for ‘polygon’
filterMarkS4: no visible global function definition for ‘quantile’
genomeAberration: no visible global function definition for ‘dev.cur’
genomeAberration: no visible global function definition for ‘dev.new’
genomeAberration: no visible global function definition for ‘par’
genomeAberration: no visible global function definition for ‘plot’
genomeAberration: no visible global function definition for ‘rect’
genomeAberration: no visible global function definition for ‘title’
genomeAberration: no visible global function definition for ‘axis’
genomeAberration: no visible global function definition for ‘abline’
genomeAberration: no visible global function definition for
‘devAskNewPage’
genomeFreq: no visible global function definition for ‘dev.cur’
genomeFreq: no visible global function definition for ‘dev.new’
genomeFreq: no visible global function definition for ‘par’
genomeFreq: no visible global function definition for ‘plot’
genomeFreq: no visible global function definition for ‘title’
genomeFreq: no visible global function definition for ‘rect’
genomeFreq: no visible global function definition for ‘abline’
genomeFreq: no visible global function definition for ‘devAskNewPage’
genomeHeat: no visible global function definition for ‘dev.cur’
genomeHeat: no visible global function definition for ‘dev.new’
genomeHeat: no visible global function definition for ‘par’
genomeHeat: no visible global function definition for ‘plot’
genomeHeat: no visible global function definition for ‘rect’
genomeHeat: no visible global function definition for ‘title’
genomeHeat: no visible global function definition for ‘axis’
genomeHeat: no visible global function definition for ‘abline’
genomeHeat: no visible global function definition for ‘devAskNewPage’
getFreqPlotParameters: no visible global function definition for
‘modifyList’
getHeatParameters: no visible global function definition for
‘modifyList’
getMad: no visible global function definition for ‘mad’
getPlotParameters: no visible global function definition for ‘rainbow’
getPlotParameters: no visible global function definition for
‘modifyList’
madWins: no visible global function definition for ‘mad’
medianFilter: no visible global function definition for ‘runmed’
multipcf: no visible global function definition for ‘read.table’
multipcf: no visible global function definition for ‘write.table’
pcf: no visible global function definition for ‘read.table’
pcf: no visible global function definition for ‘write.table’
pcfWins: no visible global function definition for ‘mad’
plotAllele: no visible global function definition for ‘modifyList’
plotAllele: no visible global function definition for ‘pdf’
plotAllele: no visible global function definition for ‘dev.cur’
plotAllele: no visible global function definition for ‘dev.new’
plotAllele: no visible global function definition for ‘devAskNewPage’
plotAllele: no visible global function definition for ‘quantile’
plotAllele: no visible global function definition for ‘par’
plotAllele: no visible global function definition for ‘legend’
plotAllele: no visible global function definition for ‘title’
plotAllele: no visible global function definition for ‘graphics.off’
plotChrom: no visible global function definition for ‘pdf’
plotChrom: no visible global function definition for ‘dev.cur’
plotChrom: no visible global function definition for ‘dev.new’
plotChrom: no visible global function definition for ‘devAskNewPage’
plotChrom: no visible global function definition for ‘quantile’
plotChrom: no visible global function definition for ‘par’
plotChrom: no visible global function definition for ‘legend’
plotChrom: no visible global function definition for ‘title’
plotChrom: no visible global function definition for ‘graphics.off’
plotCircle: no visible global function definition for ‘par’
plotCircle: no visible global function definition for ‘plot’
plotCircle: no visible global function definition for ‘text’
plotCircle: no visible global function definition for ‘xspline’
plotCircle: no visible global function definition for ‘lines’
plotGamma: no visible global function definition for ‘quantile’
plotGamma: no visible global function definition for ‘col2rgb’
plotGamma: no visible global function definition for ‘rgb’
plotGamma: no visible global function definition for ‘dev.cur’
plotGamma: no visible global function definition for ‘dev.new’
plotGamma: no visible global function definition for ‘par’
plotGamma: no visible global function definition for ‘plot’
plotGamma: no visible global function definition for ‘axis’
plotGamma: no visible global function definition for ‘box’
plotGamma: no visible global function definition for ‘legend’
plotGamma: no visible global function definition for ‘barplot’
plotGamma: no visible global function definition for ‘abline’
plotGamma: no visible global function definition for ‘mtext’
plotGamma: no visible global function definition for ‘points’
plotGenome: no visible global function definition for ‘quantile’
plotGenome: no visible global function definition for ‘pdf’
plotGenome: no visible global function definition for ‘dev.cur’
plotGenome: no visible global function definition for ‘dev.new’
plotGenome: no visible global function definition for ‘par’
plotGenome: no visible global function definition for ‘legend’
plotGenome: no visible global function definition for ‘title’
plotGenome: no visible global function definition for ‘devAskNewPage’
plotGenome: no visible global function definition for ‘graphics.off’
plotIdeogram: no visible global function definition for ‘plot’
plotIdeogram: no visible global function definition for ‘rect’
plotIdeogram: no visible global function definition for ‘mtext’
plotObs: no visible global function definition for ‘par’
plotObs: no visible global function definition for ‘plot’
plotSample: no visible global function definition for ‘pdf’
plotSample: no visible global function definition for ‘dev.cur’
plotSample: no visible global function definition for ‘dev.new’
plotSample: no visible global function definition for ‘devAskNewPage’
plotSample: no visible global function definition for ‘quantile’
plotSample: no visible global function definition for ‘par’
plotSample: no visible global function definition for ‘legend’
plotSample: no visible global function definition for ‘title’
plotSample: no visible global function definition for ‘graphics.off’
plotSegments: no visible global function definition for ‘par’
plotSegments: no visible global function definition for ‘plot’
sawMarkM: no visible global function definition for ‘quantile’
subset.abe: no visible binding for global variable ‘quantile’
subsetData: no visible global function definition for ‘read.table’
subsetSegments: no visible global function definition for ‘read.table’
winsorize: no visible global function definition for ‘read.table’
winsorize: no visible global function definition for ‘write.table’
Undefined global functions or variables:
abline axis barplot box col2rgb colorRampPalette dev.cur dev.new
devAskNewPage graphics.off legend lines mad modifyList mtext par pdf
plot points polygon quantile rainbow read.table rect rgb runmed
segments text title write.table xspline
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.cur",
"dev.new", "devAskNewPage", "graphics.off", "pdf",
"rainbow", "rgb")
importFrom("graphics", "abline", "axis", "barplot", "box", "legend",
"lines", "mtext", "par", "plot", "points", "polygon",
"rect", "segments", "text", "title", "xspline")
importFrom("stats", "mad", "quantile", "runmed")
importFrom("utils", "modifyList", "read.table", "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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCircle 10.098 0.920 11.081
plotFreq 5.366 0.300 5.870
plotHeatmap 5.012 0.223 5.430
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/copynumber.Rcheck/00check.log’
for details.
copynumber.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL copynumber ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘copynumber’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (copynumber)
copynumber.Rcheck/copynumber-Ex.timings
| name | user | system | elapsed | |
| SNPdata | 0.015 | 0.005 | 0.020 | |
| aspcf | 2.720 | 0.345 | 3.065 | |
| callAberrations | 3.767 | 0.345 | 4.112 | |
| getGRangesFormat | 3.594 | 0.292 | 3.886 | |
| imputeMissing | 2.746 | 0.159 | 2.904 | |
| interpolate.pcf | 0.648 | 0.049 | 0.698 | |
| lymphoma | 0.001 | 0.001 | 0.003 | |
| micma | 0.001 | 0.002 | 0.003 | |
| multipcf | 0.945 | 0.061 | 1.006 | |
| pcf | 0.930 | 0.027 | 0.958 | |
| pcfPlain | 0.161 | 0.045 | 0.205 | |
| plotAberration | 4.149 | 0.247 | 4.398 | |
| plotAllele | 3.235 | 0.316 | 3.567 | |
| plotChrom | 3.281 | 0.187 | 3.471 | |
| plotCircle | 10.098 | 0.920 | 11.081 | |
| plotFreq | 5.366 | 0.300 | 5.870 | |
| plotGamma | 1.795 | 0.378 | 2.175 | |
| plotGenome | 4.302 | 0.174 | 4.622 | |
| plotHeatmap | 5.012 | 0.223 | 5.430 | |
| plotSample | 3.927 | 0.144 | 4.207 | |
| selectSegments | 1.029 | 0.061 | 1.090 | |
| subsetData | 0.007 | 0.002 | 0.008 | |
| subsetSegments | 4.066 | 0.237 | 4.304 | |
| winsorize | 0.477 | 0.017 | 0.494 | |