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CHECK report for CNVRanger on merida1

This page was generated on 2021-05-06 12:34:35 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the CNVRanger package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 342/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVRanger 1.6.1  (landing page)
Ludwig Geistlinger
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/CNVRanger
Branch: RELEASE_3_12
Last Commit: a995fa8
Last Changed Date: 2020-12-09 15:36:10 -0400 (Wed, 09 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CNVRanger
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNVRanger_1.6.1.tar.gz
StartedAt: 2021-05-06 00:28:15 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:32:59 -0400 (Thu, 06 May 2021)
EllapsedTime: 284.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVRanger.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNVRanger_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CNVRanger.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVRanger/DESCRIPTION’ ... OK
* this is package ‘CNVRanger’ version ‘1.6.1’
* package encoding: UTF-8
* 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 ‘CNVRanger’ 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
Unexported object imported by a ':::' call: 'rappdirs:::get_os'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRecurrentRegions: no visible binding for global variable ‘type’
plotRecurrentRegions: no visible binding for global variable ‘pvalue’
Undefined global functions or variables:
  pvalue type
* 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
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
plotRecurrentRegions 20.192  0.067  29.291
plotEQTL             19.055  0.582  31.985
plotManhattan         7.849  0.098   7.964
cnvGWAS               7.604  0.110   7.810
* 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-3.12-bioc/meat/CNVRanger.Rcheck/00check.log’
for details.



Installation output

CNVRanger.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNVRanger
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CNVRanger’ ...
** using staged installation
** R
** 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 (CNVRanger)

Tests output


Example timings

CNVRanger.Rcheck/CNVRanger-Ex.timings

nameusersystemelapsed
cnvEQTL2.9070.1123.024
cnvGWAS7.6040.1107.810
cnvOncoPrint2.6920.0362.730
generateGDS1.0550.0311.088
importLrrBaf0.0170.0050.022
plotEQTL19.055 0.58231.985
plotManhattan7.8490.0987.964
plotRecurrentRegions20.192 0.06729.291
populationRanges2.3040.0102.320
setupCnvGWAS0.0130.0040.017