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CHECK report for IMPCdata on merida1

This page was generated on 2021-05-06 12:35:22 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the IMPCdata package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 888/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IMPCdata 1.26.0  (landing page)
Jeremy Mason
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/IMPCdata
Branch: RELEASE_3_12
Last Commit: 070c677
Last Changed Date: 2020-10-27 11:00:23 -0400 (Tue, 27 Oct 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: IMPCdata
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IMPCdata.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IMPCdata_1.26.0.tar.gz
StartedAt: 2021-05-06 02:49:26 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:51:14 -0400 (Thu, 06 May 2021)
EllapsedTime: 107.6 seconds
RetCode: 0
Status:   OK  
CheckDir: IMPCdata.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:IMPCdata.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IMPCdata_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/IMPCdata.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 ‘IMPCdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IMPCdata’ version ‘1.26.0’
* 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 ‘IMPCdata’ 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 ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
getPhenCenters 0.199  0.022  13.563
getProcedures  0.086  0.009   5.440
getStrains     0.075  0.008   6.147
printStrains   0.069  0.009  10.245
getIMPCDataset 0.021  0.004   6.888
* 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: OK


Installation output

IMPCdata.Rcheck/00install.out

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

Tests output


Example timings

IMPCdata.Rcheck/IMPCdata-Ex.timings

nameusersystemelapsed
getAlleles0.0940.0133.265
getGenes0.0880.0093.361
getIMPCDataset0.0210.0046.888
getIMPCTable0.0640.0122.755
getName0.0160.0021.014
getParameters0.1010.0103.508
getPhenCenters 0.199 0.02213.563
getPipelines0.0900.0094.798
getProcedures0.0860.0095.440
getStrains0.0750.0086.147
getZygosities0.0210.0020.489
printAlleles0.0780.0093.340
printGenes0.0720.0083.271
printParameters0.0840.0083.388
printPhenCenters0.0260.0033.861
printPipelines0.0830.0084.558
printProcedures0.0780.0084.881
printStrains 0.069 0.00910.245