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CHECK report for copynumber on tokay1

This page was generated on 2019-04-13 11:22:48 -0400 (Sat, 13 Apr 2019).

Package 326/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
copynumber 1.22.0
Gro Nilsen
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/copynumber
Branch: RELEASE_3_8
Last Commit: 9273073
Last Changed Date: 2018-10-30 11:41:51 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: copynumber
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:copynumber.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings copynumber_1.22.0.tar.gz
StartedAt: 2019-04-13 01:28:57 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:32:47 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 230.4 seconds
RetCode: 0
Status:  OK  
CheckDir: copynumber.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:copynumber.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings copynumber_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/copynumber.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'copynumber/DESCRIPTION' ... OK
* this is package 'copynumber' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 '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
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
plotCircle 5.11   0.08    5.19
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/copynumber.Rcheck/00check.log'
for details.



Installation output

copynumber.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/copynumber_1.22.0.tar.gz && rm -rf copynumber.buildbin-libdir && mkdir copynumber.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=copynumber.buildbin-libdir copynumber_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL copynumber_1.22.0.zip && rm copynumber_1.22.0.tar.gz copynumber_1.22.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  770k  100  770k    0     0  16.4M      0 --:--:-- --:--:-- --:--:-- 17.9M

install for i386

* installing *source* package 'copynumber' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'copynumber'
    finding HTML links ... done
    SNPdata                                 html  
    aspcf                                   html  
    callAberrations                         html  
    getGRangesFormat                        html  
    imputeMissing                           html  
    interpolate.pcf                         html  
    lymphoma                                html  
    micma                                   html  
    multipcf                                html  
    pcf                                     html  
    pcfPlain                                html  
    plotAberration                          html  
    plotAllele                              html  
    plotChrom                               html  
    plotCircle                              html  
    plotFreq                                html  
    plotGamma                               html  
    plotGenome                              html  
    plotHeatmap                             html  
    plotSample                              html  
    selectSegments                          html  
    subsetData                              html  
    subsetSegments                          html  
    winsorize                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'copynumber' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'copynumber' as copynumber_1.22.0.zip
* DONE (copynumber)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'copynumber' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

copynumber.Rcheck/examples_i386/copynumber-Ex.timings

nameusersystemelapsed
SNPdata0.030.000.03
aspcf1.630.061.69
callAberrations1.860.031.89
getGRangesFormat1.860.021.88
imputeMissing1.330.001.33
interpolate.pcf0.260.000.27
lymphoma0.000.010.01
micma000
multipcf0.440.000.44
pcf0.510.000.52
pcfPlain0.100.000.09
plotAberration1.870.021.89
plotAllele2.570.062.63
plotChrom1.450.021.47
plotCircle4.560.174.73
plotFreq2.290.002.29
plotGamma1.110.011.13
plotGenome3.180.023.18
plotHeatmap1.950.031.99
plotSample2.110.022.12
selectSegments0.50.00.5
subsetData000
subsetSegments1.70.01.7
winsorize0.20.00.2

copynumber.Rcheck/examples_x64/copynumber-Ex.timings

nameusersystemelapsed
SNPdata0.020.010.03
aspcf1.500.041.53
callAberrations1.800.001.79
getGRangesFormat1.810.001.82
imputeMissing1.390.001.39
interpolate.pcf0.280.010.29
lymphoma000
micma000
multipcf0.520.000.52
pcf0.550.000.55
pcfPlain0.090.000.09
plotAberration2.250.022.27
plotAllele2.700.012.72
plotChrom1.520.031.54
plotCircle5.110.085.19
plotFreq2.390.022.41
plotGamma0.970.031.00
plotGenome3.060.063.12
plotHeatmap2.080.022.09
plotSample2.200.032.24
selectSegments0.530.000.53
subsetData000
subsetSegments1.770.001.77
winsorize0.470.000.46