Package: cellbaseR

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2018-10-06 01:02:44 -0400 (Sat, 06 Oct 2018)

EndedAt: 2018-10-06 01:05:41 -0400 (Sat, 06 Oct 2018)

EllapsedTime: 177.2 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/cellbaseR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.4.0’
* 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 or elapsed time > 5s
                              user system elapsed
AnnotateVcf-CellBaseR-method 9.912  3.718  13.933
* 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/3.5/Resources/library’
* installing *source* package ‘cellbaseR’ ...
** 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
* DONE (cellbaseR)

name	user	system	elapsed
AnnotateVcf-CellBaseR-method	9.912	3.718	13.933
CellBaseParam	0.003	0.001	0.004
CellBaseR	0.042	0.006	0.361
createGeneModel	0.337	0.049	1.037
getCaddScores	0.056	0.007	0.571
getCellBase-CellBaseR-method	0.067	0.008	0.593
getCellBaseResourceHelp	0.292	0.035	0.935
getChromosomeInfo-CellBaseR-method	0.054	0.004	0.565
getClinical-CellBaseR-method	0.743	0.028	1.601
getClinicalByRegion	1.358	0.087	2.582
getConservationByRegion	0.064	0.004	0.726
getGene-CellBaseR-method	0.103	0.005	0.752
getGeneInfo	0.051	0.002	0.568
getMeta-CellBaseR-method	0.057	0.003	0.567
getProtein-CellBaseR-method	0.112	0.005	0.740
getProteinInfo	0.115	0.010	0.739
getRegion-CellBaseR-method	0.094	0.005	0.841
getRegulatoryByRegion	0.120	0.006	1.028
getSnp-CellBaseR-method	0.052	0.002	0.565
getSnpByGene	0.058	0.002	0.579
getTf-CellBaseR-method	0.041	0.002	2.861
getTfbsByRegion	0.058	0.003	0.605
getTranscript-CellBaseR-method	0.044	0.002	0.561
getTranscriptByGene	0.042	0.002	0.558
getVariant-CellBaseR-method	0.110	0.008	0.796
getVariantAnnotation	0.101	0.003	0.792
getXref-CellBaseR-method	0.043	0.002	0.558