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CHECK report for cellbaseR on celaya2

This page was generated on 2020-01-16 13:47:55 -0500 (Thu, 16 Jan 2020).

Package 238/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.11.0
Mohammed OE Abdallah
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: master
Last Commit: 69e4670
Last Changed Date: 2019-10-29 13:42:19 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  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: cellbaseR
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellbaseR_1.11.0.tar.gz
StartedAt: 2020-01-16 02:34:50 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 02:38:35 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 224.3 seconds
RetCode: 0
Status:  OK 
CheckDir: cellbaseR.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:cellbaseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellbaseR_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/cellbaseR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellbaseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellbaseR’ version ‘1.11.0’
* 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 ‘cellbaseR’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
AnnotateVcf-CellBaseR-method 9.257  4.202  11.737
* 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

cellbaseR.Rcheck/00install.out

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

Tests output


Example timings

cellbaseR.Rcheck/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 9.257 4.20211.737
CellBaseParam0.0030.0000.005
CellBaseR0.0480.0100.373
createGeneModel0.6710.1871.464
getCaddScores0.0510.0050.551
getCellBase-CellBaseR-method0.0510.0040.540
getCellBaseResourceHelp0.1790.0080.759
getChromosomeInfo-CellBaseR-method0.0450.0050.526
getClinical-CellBaseR-method0.8970.0671.751
getClinicalByRegion2.1750.0973.498
getConservationByRegion0.1000.0110.830
getGene-CellBaseR-method0.1690.0110.787
getGeneInfo0.0730.0080.570
getMeta-CellBaseR-method0.0780.0070.571
getProtein-CellBaseR-method0.1790.0070.760
getProteinInfo0.1740.0050.754
getRegion-CellBaseR-method0.1470.0061.858
getRegulatoryByRegion0.1770.0091.028
getSnp-CellBaseR-method0.1030.0050.587
getSnpByGene0.0930.0050.591
getTf-CellBaseR-method0.0600.0052.924
getTfbsByRegion0.0860.0050.618
getTranscript-CellBaseR-method0.0650.0050.553
getTranscriptByGene0.0600.0060.560
getVariant-CellBaseR-method0.1580.0110.831
getVariantAnnotation0.1910.0120.826
getXref-CellBaseR-method0.0560.0030.536