Package: cellbaseR

Version: 1.4.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cellbaseR_1.4.0.tar.gz

StartedAt: 2018-10-15 23:02:43 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 23:04:32 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 108.5 seconds

RetCode: 0

Status:  OK

CheckDir: cellbaseR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cellbaseR_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/cellbaseR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.4.0’
* 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 6.292   1.48  10.375
* 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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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL cellbaseR
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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	6.292	1.480	10.375
CellBaseParam	0.004	0.000	0.002
CellBaseR	0.036	0.012	0.341
createGeneModel	0.328	0.012	0.963
getCaddScores	0.064	0.000	0.547
getCellBase-CellBaseR-method	0.060	0.004	0.559
getCellBaseResourceHelp	0.316	0.016	0.913
getChromosomeInfo-CellBaseR-method	0.052	0.000	0.533
getClinical-CellBaseR-method	0.520	0.004	1.352
getClinicalByRegion	1.084	0.052	2.283
getConservationByRegion	0.092	0.004	0.815
getGene-CellBaseR-method	0.148	0.000	0.868
getGeneInfo	0.072	0.000	0.574
getMeta-CellBaseR-method	0.080	0.004	0.562
getProtein-CellBaseR-method	0.164	0.000	0.741
getProteinInfo	0.156	0.000	1.759
getRegion-CellBaseR-method	0.148	0.000	0.866
getRegulatoryByRegion	0.132	0.000	0.984
getSnp-CellBaseR-method	0.076	0.004	0.578
getSnpByGene	0.072	0.000	0.612
getTf-CellBaseR-method	0.052	0.000	2.792
getTfbsByRegion	0.088	0.000	0.618
getTranscript-CellBaseR-method	0.056	0.000	0.552
getTranscriptByGene	0.056	0.000	1.554
getVariant-CellBaseR-method	0.112	0.000	0.758
getVariantAnnotation	0.152	0.000	0.810
getXref-CellBaseR-method	0.064	0.004	0.563