Package: cellbaseR

Version: 1.8.1

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_1.8.1.tar.gz

StartedAt: 2019-10-16 01:13:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:17:17 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 198.7 seconds

RetCode: 0

Status:  OK

CheckDir: cellbaseR.Rcheck

Warnings: 0

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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_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cellbaseR.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 ‘cellbaseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellbaseR’ version ‘1.8.1’
* 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 or elapsed time > 5s
                               user system elapsed
AnnotateVcf-CellBaseR-method 16.984  8.983  21.546
* 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

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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/3.6/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)

name	user	system	elapsed
AnnotateVcf-CellBaseR-method	16.984	8.983	21.546
CellBaseParam	0.005	0.002	0.008
CellBaseR	0.062	0.013	0.373
createGeneModel	0.293	0.061	0.975
getCaddScores	0.074	0.013	0.579
getCellBase-CellBaseR-method	0.091	0.015	0.615
getCellBaseResourceHelp	0.419	0.091	1.092
getChromosomeInfo-CellBaseR-method	0.074	0.012	0.577
getClinical-CellBaseR-method	1.286	0.093	2.205
getClinicalByRegion	2.249	0.124	3.632
getConservationByRegion	0.104	0.010	0.846
getGene-CellBaseR-method	0.192	0.013	0.858
getGeneInfo	0.077	0.007	0.598
getMeta-CellBaseR-method	0.080	0.006	0.572
getProtein-CellBaseR-method	0.195	0.021	0.901
getProteinInfo	0.205	0.006	0.807
getRegion-CellBaseR-method	0.125	0.009	0.872
getRegulatoryByRegion	0.166	0.013	1.038
getSnp-CellBaseR-method	0.081	0.004	0.577
getSnpByGene	0.102	0.004	0.612
getTf-CellBaseR-method	0.064	0.005	2.993
getTfbsByRegion	0.073	0.006	0.605
getTranscript-CellBaseR-method	0.079	0.007	0.585
getTranscriptByGene	0.059	0.004	0.562
getVariant-CellBaseR-method	0.157	0.007	0.817
getVariantAnnotation	0.165	0.010	0.833
getXref-CellBaseR-method	0.046	0.004	0.540