Package: cellbaseR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellbaseR_1.2.0.tar.gz

StartedAt: 2018-04-12 01:23:40 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:25:52 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 131.4 seconds

RetCode: 0

Status:  OK

CheckDir: cellbaseR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellbaseR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cellbaseR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
AnnotateVcf-CellBaseR-method 3.286  0.925  13.742
* 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

* installing *source* package ‘cellbaseR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cellbaseR)

name	user	system	elapsed
AnnotateVcf-CellBaseR-method	3.286	0.925	13.742
CellBaseParam	0.002	0.000	0.002
CellBaseR	0.046	0.002	0.339
createGeneModel	0.448	0.026	1.075
getCaddScores	0.078	0.003	0.572
getCellBase-CellBaseR-method	0.048	0.002	0.591
getCellBaseResourceHelp	0.207	0.003	0.818
getChromosomeInfo-CellBaseR-method	0.041	0.002	0.530
getClinical-CellBaseR-method	0.659	0.021	1.467
getClinicalByRegion	1.145	0.046	2.178
getConservationByRegion	0.074	0.004	0.682
getGene-CellBaseR-method	0.092	0.004	0.740
getGeneInfo	0.049	0.002	0.538
getMeta-CellBaseR-method	0.061	0.003	0.565
getProtein-CellBaseR-method	0.098	0.002	0.692
getProteinInfo	0.111	0.003	0.699
getRegion-CellBaseR-method	0.091	0.003	0.859
getRegulatoryByRegion	0.112	0.003	0.986
getSnp-CellBaseR-method	0.053	0.001	0.548
getSnpByGene	0.058	0.002	0.592
getTf-CellBaseR-method	0.042	0.002	2.493
getTfbsByRegion	0.056	0.002	0.564
getTranscript-CellBaseR-method	0.046	0.002	0.539
getTranscriptByGene	0.038	0.002	0.530
getVariant-CellBaseR-method	0.116	0.008	0.737
getVariantAnnotation	0.095	0.003	0.710
getXref-CellBaseR-method	0.034	0.001	0.525