Package: cellbaseR

Version: 1.11.0

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_1.11.0.tar.gz

StartedAt: 2020-01-16 02:34:50 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:38:35 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 224.3 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 --install=check:cellbaseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellbaseR_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/cellbaseR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.11.0’
* 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 (user + system) or elapsed time > 5s
                              user system elapsed
AnnotateVcf-CellBaseR-method 9.257  4.202  11.737
* 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/4.0/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	9.257	4.202	11.737
CellBaseParam	0.003	0.000	0.005
CellBaseR	0.048	0.010	0.373
createGeneModel	0.671	0.187	1.464
getCaddScores	0.051	0.005	0.551
getCellBase-CellBaseR-method	0.051	0.004	0.540
getCellBaseResourceHelp	0.179	0.008	0.759
getChromosomeInfo-CellBaseR-method	0.045	0.005	0.526
getClinical-CellBaseR-method	0.897	0.067	1.751
getClinicalByRegion	2.175	0.097	3.498
getConservationByRegion	0.100	0.011	0.830
getGene-CellBaseR-method	0.169	0.011	0.787
getGeneInfo	0.073	0.008	0.570
getMeta-CellBaseR-method	0.078	0.007	0.571
getProtein-CellBaseR-method	0.179	0.007	0.760
getProteinInfo	0.174	0.005	0.754
getRegion-CellBaseR-method	0.147	0.006	1.858
getRegulatoryByRegion	0.177	0.009	1.028
getSnp-CellBaseR-method	0.103	0.005	0.587
getSnpByGene	0.093	0.005	0.591
getTf-CellBaseR-method	0.060	0.005	2.924
getTfbsByRegion	0.086	0.005	0.618
getTranscript-CellBaseR-method	0.065	0.005	0.553
getTranscriptByGene	0.060	0.006	0.560
getVariant-CellBaseR-method	0.158	0.011	0.831
getVariantAnnotation	0.191	0.012	0.826
getXref-CellBaseR-method	0.056	0.003	0.536