Package: cellbaseR

Version: 1.7.0

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_1.7.0.tar.gz

StartedAt: 2019-03-29 00:24:56 -0400 (Fri, 29 Mar 2019)

EndedAt: 2019-03-29 00:28:12 -0400 (Fri, 29 Mar 2019)

EllapsedTime: 195.1 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cellbaseR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.7.0’
* 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 or elapsed time > 5s
                               user system elapsed
AnnotateVcf-CellBaseR-method 13.618  7.711  17.617
* 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	13.618	7.711	17.617
CellBaseParam	0.004	0.003	0.007
CellBaseR	0.050	0.011	0.347
createGeneModel	0.472	0.098	1.163
getCaddScores	0.068	0.014	0.551
getCellBase-CellBaseR-method	0.073	0.017	0.576
getCellBaseResourceHelp	0.303	0.077	0.946
getChromosomeInfo-CellBaseR-method	0.061	0.007	0.539
getClinical-CellBaseR-method	0.981	0.063	1.836
getClinicalByRegion	2.607	0.289	4.092
getConservationByRegion	0.107	0.014	0.823
getGene-CellBaseR-method	0.154	0.018	0.869
getGeneInfo	0.070	0.005	0.549
getMeta-CellBaseR-method	0.084	0.006	0.574
getProtein-CellBaseR-method	0.185	0.011	0.774
getProteinInfo	0.176	0.006	0.757
getRegion-CellBaseR-method	0.166	0.009	0.875
getRegulatoryByRegion	0.193	0.012	1.042
getSnp-CellBaseR-method	0.085	0.005	0.572
getSnpByGene	0.103	0.004	0.600
getTf-CellBaseR-method	0.066	0.004	2.915
getTfbsByRegion	0.093	0.009	0.612
getTranscript-CellBaseR-method	0.066	0.005	0.556
getTranscriptByGene	0.065	0.004	0.550
getVariant-CellBaseR-method	0.181	0.009	0.818
getVariantAnnotation	0.176	0.007	0.826
getXref-CellBaseR-method	0.062	0.006	0.540