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CHECK report for CopywriteR on malbec2

This page was generated on 2019-10-16 12:06:34 -0400 (Wed, 16 Oct 2019).

Package 345/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopywriteR 2.16.0
Oscar Krijgsman
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CopywriteR
Branch: RELEASE_3_9
Last Commit: be03a5b
Last Changed Date: 2019-05-02 11:53:54 -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: CopywriteR
Version: 2.16.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CopywriteR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CopywriteR_2.16.0.tar.gz
StartedAt: 2019-10-16 00:49:45 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:52:57 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 192.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CopywriteR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CopywriteR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CopywriteR_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CopywriteR.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 ‘CopywriteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CopywriteR’ version ‘2.16.0’
* 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 ‘CopywriteR’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.peakCutoff: no visible global function definition for ‘dpois’
.peakCutoff: no visible global function definition for ‘ppois’
.tng: no visible global function definition for ‘png’
.tng: no visible global function definition for ‘par’
.tng: no visible global function definition for ‘dev.off’
.tng: no visible global function definition for ‘loess’
.tng: no visible global function definition for ‘predict’
.tng: no visible global function definition for ‘points’
.tng: no visible global function definition for ‘rgb’
.tng: no visible global function definition for ‘lines’
CopywriteR: no visible global function definition for ‘as’
CopywriteR: no visible global function definition for ‘packageVersion’
CopywriteR: no visible global function definition for ‘getClass’
CopywriteR : DetectPeaks: no visible global function definition for
  ‘as’
CopywriteR : DetectPeaks: no visible global function definition for
  ‘write.table’
CopywriteR : CalculateDepthOfCoverage: no visible global function
  definition for ‘read.table’
CopywriteR : CalculateDepthOfCoverage: no visible global function
  definition for ‘as’
CopywriteR: no visible global function definition for ‘write.table’
CopywriteR: no visible global function definition for ‘pdf’
CopywriteR: no visible global function definition for ‘plot’
CopywriteR: no visible global function definition for ‘ecdf’
CopywriteR: no visible global function definition for ‘dev.off’
CopywriteR: no visible global function definition for ‘read.table’
plotCNA: no visible global function definition for ‘read.table’
plotCNA :  : : no visible global function
  definition for ‘pdf’
plotCNA :  : : no visible global function
  definition for ‘plot’
plotCNA :  : : no visible global function
  definition for ‘points’
plotCNA :  :  : : no visible global
  function definition for ‘segments’
plotCNA :  : : no visible global function
  definition for ‘par’
plotCNA :  : : no visible global function
  definition for ‘text’
plotCNA :  : : no visible global function
  definition for ‘axis’
plotCNA :  : : no visible global function
  definition for ‘abline’
plotCNA :  : : no visible global function
  definition for ‘dev.off’
preCopywriteR: no visible global function definition for ‘as’
Undefined global functions or variables:
  abline as axis dev.off dpois ecdf getClass lines loess packageVersion
  par pdf plot png points ppois predict read.table rgb segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "png", "rgb")
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "segments", "text")
  importFrom("methods", "as", "getClass")
  importFrom("stats", "dpois", "ecdf", "loess", "ppois", "predict")
  importFrom("utils", "packageVersion", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/CopywriteR.Rcheck/00check.log’
for details.



Installation output

CopywriteR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CopywriteR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CopywriteR’ ...
** using staged installation
** R
** 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 (CopywriteR)

Tests output


Example timings

CopywriteR.Rcheck/CopywriteR-Ex.timings

nameusersystemelapsed
CopywriteR000
plotCNA0.0000.0000.001
preCopywriteR000