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CHECK report for IMPCdata on celaya2

This page was generated on 2019-10-16 12:54:25 -0400 (Wed, 16 Oct 2019).

Package 808/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IMPCdata 1.20.0
Jeremy Mason
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/IMPCdata
Branch: RELEASE_3_9
Last Commit: 7cda8d3
Last Changed Date: 2019-05-02 11:53:50 -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: IMPCdata
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2019-10-16 03:48:54 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:51:06 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 132.1 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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IMPCdata.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.20.0’
* 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 or elapsed time > 5s
                 user system elapsed
getPhenCenters  0.301  0.029  14.507
getAlleles      0.247  0.037   5.089
printStrains    0.234  0.023   9.461
getStrains      0.233  0.023  10.629
getParameters   0.146  0.013   5.134
printProcedures 0.133  0.014   6.433
* 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/3.6/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
getAlleles0.2470.0375.089
getGenes0.2240.0244.847
getIMPCDataset1.0570.0604.138
getIMPCTable0.1210.0214.422
getName0.0250.0031.031
getParameters0.1460.0135.134
getPhenCenters 0.301 0.02914.507
getPipelines0.1170.0113.683
getProcedures0.1540.0134.657
getStrains 0.233 0.02310.629
getZygosities0.0290.0031.060
printAlleles0.1280.0124.450
printGenes0.1280.0113.312
printParameters0.1360.0134.760
printPhenCenters0.0420.0064.149
printPipelines0.1110.0114.445
printProcedures0.1330.0146.433
printStrains0.2340.0239.461