Package: cellbaseR

Version: 1.2.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cellbaseR_1.2.0.tar.gz

StartedAt: 2018-04-11 22:03:54 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:06:03 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 128.8 seconds

RetCode: 0

Status:  OK

CheckDir: cellbaseR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cellbaseR_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/cellbaseR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.0’
* 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 2.948  0.444  12.425
* 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	2.948	0.444	12.425
CellBaseParam	0.000	0.000	0.002
CellBaseR	0.036	0.004	0.317
createGeneModel	0.712	0.020	1.322
getCaddScores	0.104	0.004	0.569
getCellBase-CellBaseR-method	0.056	0.000	0.521
getCellBaseResourceHelp	0.540	0.000	1.077
getChromosomeInfo-CellBaseR-method	0.040	0.004	0.499
getClinical-CellBaseR-method	0.908	0.000	1.723
getClinicalByRegion	0.760	0.004	1.818
getConservationByRegion	0.088	0.000	0.775
getGene-CellBaseR-method	0.148	0.004	0.817
getGeneInfo	0.080	0.004	0.545
getMeta-CellBaseR-method	0.056	0.004	0.522
getProtein-CellBaseR-method	0.144	0.000	0.686
getProteinInfo	0.144	0.004	0.706
getRegion-CellBaseR-method	0.088	0.008	0.764
getRegulatoryByRegion	0.160	0.000	1.037
getSnp-CellBaseR-method	0.056	0.000	0.517
getSnpByGene	0.10	0.00	0.57
getTf-CellBaseR-method	0.064	0.000	4.843
getTfbsByRegion	0.068	0.000	0.553
getTranscript-CellBaseR-method	0.072	0.000	0.534
getTranscriptByGene	0.064	0.000	0.527
getVariant-CellBaseR-method	0.152	0.000	0.757
getVariantAnnotation	0.148	0.004	0.761
getXref-CellBaseR-method	0.064	0.000	0.525