BioC 3.5: CHECK report for cellbaseR on toluca2

Package: cellbaseR

Version: 0.99.39

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellbaseR_0.99.39.tar.gz

StartedAt: 2017-04-23 01:26:43 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 01:30:11 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 208.3 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 --no-vignettes --timings cellbaseR_0.99.39.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/cellbaseR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘0.99.39’
* 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
getClinical-CellBaseR-method 17.367  0.157  19.918
getClinicalByRegion           7.714  0.069   9.232
AnnotateVcf-CellBaseR-method  3.942  0.662  18.073
getTf-CellBaseR-method        0.157  0.001  18.412
* 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	3.942	0.662	18.073
CellBaseParam	0.002	0.000	0.002
CellBaseR	0.133	0.004	0.408
createGeneModel	0.544	0.024	1.190
getCaddScores	0.204	0.002	0.670
getCellBase-CellBaseR-method	0.160	0.002	0.647
getCellBaseResourceHelp	0.337	0.003	0.895
getChromosomeInfo-CellBaseR-method	0.131	0.001	0.595
getClinical-CellBaseR-method	17.367	0.157	19.918
getClinicalByGene	2.219	0.031	3.031
getClinicalByRegion	7.714	0.069	9.232
getConservationByRegion	0.194	0.003	3.267
getGene-CellBaseR-method	0.242	0.004	1.074
getGeneInfo	0.153	0.002	0.628
getMeta-CellBaseR-method	0.174	0.002	0.644
getProtein-CellBaseR-method	0.250	0.002	1.338
getProteinInfo	0.255	0.003	1.186
getRegion-CellBaseR-method	0.212	0.003	1.118
getRegulatoryByRegion	0.263	0.005	1.179
getSnp-CellBaseR-method	0.243	0.004	0.732
getSnpByGene	0.190	0.001	0.661
getTf-CellBaseR-method	0.157	0.001	18.412
getTfbsByRegion	0.176	0.001	4.214
getTranscript-CellBaseR-method	0.168	0.002	0.652
getTranscriptByGene	0.149	0.001	0.619
getVariant-CellBaseR-method	0.249	0.002	0.994
getVariantAnnotation	0.224	0.003	0.896
getXref-CellBaseR-method	0.155	0.002	0.773