Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:07:16 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 CopywriteR on merida1


To the developers/maintainers of the CopywriteR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CopywriteR.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 410/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopywriteR 2.28.0  (landing page)
Oscar Krijgsman
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/CopywriteR
git_branch: RELEASE_3_15
git_last_commit: 5b2a581
git_last_commit_date: 2022-04-26 11:24:54 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CopywriteR
Version: 2.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CopywriteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CopywriteR_2.28.0.tar.gz
StartedAt: 2022-06-24 01:15:36 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 01:20:57 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 321.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CopywriteR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CopywriteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CopywriteR_2.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CopywriteR.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.28.0’
* 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 ‘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 : <anonymous> : <anonymous>: no visible global function
  definition for ‘pdf’
plotCNA : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
plotCNA : <anonymous> : <anonymous> : <anonymous>: no visible global
  function definition for ‘segments’
plotCNA : <anonymous> : <anonymous>: no visible global function
  definition for ‘par’
plotCNA : <anonymous> : <anonymous>: no visible global function
  definition for ‘text’
plotCNA : <anonymous> : <anonymous>: no visible global function
  definition for ‘axis’
plotCNA : <anonymous> : <anonymous>: no visible global function
  definition for ‘abline’
plotCNA : <anonymous> : <anonymous>: 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 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", "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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/CopywriteR.Rcheck/00check.log’
for details.



Installation output

CopywriteR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CopywriteR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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
CopywriteR0.0010.0000.000
plotCNA0.0000.0000.001
preCopywriteR000