Package: cellbaseR

Version: 1.8.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cellbaseR_1.8.1.tar.gz

StartedAt: 2019-10-16 00:19:54 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:22:20 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 145.9 seconds

RetCode: 0

Status:  OK

CheckDir: cellbaseR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cellbaseR_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/cellbaseR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 10.552  1.754  12.911
getTf-CellBaseR-method        0.059  0.004   5.012
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL cellbaseR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	10.552	1.754	12.911
CellBaseParam	0.001	0.000	0.002
CellBaseR	0.039	0.011	0.346
createGeneModel	0.179	0.016	0.816
getCaddScores	0.053	0.004	0.549
getCellBase-CellBaseR-method	0.057	0.008	0.563
getCellBaseResourceHelp	0.345	0.004	0.937
getChromosomeInfo-CellBaseR-method	0.059	0.000	0.548
getClinical-CellBaseR-method	0.891	0.008	1.712
getClinicalByRegion	1.594	0.020	3.020
getConservationByRegion	0.099	0.000	0.833
getGene-CellBaseR-method	0.153	0.000	0.867
getGeneInfo	0.069	0.003	0.570
getMeta-CellBaseR-method	0.072	0.000	0.562
getProtein-CellBaseR-method	0.119	0.000	0.707
getProteinInfo	0.152	0.005	0.746
getRegion-CellBaseR-method	0.141	0.008	0.863
getRegulatoryByRegion	0.177	0.000	1.074
getSnp-CellBaseR-method	0.100	0.000	0.592
getSnpByGene	0.092	0.007	0.604
getTf-CellBaseR-method	0.059	0.004	5.012
getTfbsByRegion	0.096	0.000	0.626
getTranscript-CellBaseR-method	0.064	0.000	0.562
getTranscriptByGene	0.061	0.000	0.558
getVariant-CellBaseR-method	0.154	0.000	0.815
getVariantAnnotation	0.150	0.000	0.835
getXref-CellBaseR-method	0.056	0.003	0.552