Package: cellbaseR

Version: 1.7.2

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cellbaseR_1.7.2.tar.gz

StartedAt: 2019-04-08 23:15:34 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:17:47 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 132.7 seconds

RetCode: 0

Status:  OK

CheckDir: cellbaseR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cellbaseR_1.7.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/cellbaseR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.7.2’
* 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 8.487  1.635  10.896
* 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-3.9-bioc/R/bin/R CMD INSTALL cellbaseR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	8.487	1.635	10.896
CellBaseParam	0.003	0.000	0.003
CellBaseR	0.042	0.004	0.334
createGeneModel	0.304	0.020	0.921
getCaddScores	0.054	0.004	0.529
getCellBase-CellBaseR-method	0.083	0.008	0.571
getCellBaseResourceHelp	0.420	0.020	1.014
getChromosomeInfo-CellBaseR-method	0.052	0.000	0.522
getClinical-CellBaseR-method	0.839	0.004	1.625
getClinicalByRegion	1.993	0.040	3.229
getConservationByRegion	0.091	0.000	0.797
getGene-CellBaseR-method	0.143	0.000	0.830
getGeneInfo	0.059	0.000	0.541
getMeta-CellBaseR-method	0.071	0.000	0.543
getProtein-CellBaseR-method	0.149	0.004	0.726
getProteinInfo	0.149	0.000	0.722
getRegion-CellBaseR-method	0.103	0.008	0.802
getRegulatoryByRegion	0.174	0.000	1.005
getSnp-CellBaseR-method	0.079	0.000	0.567
getSnpByGene	0.098	0.000	0.593
getTf-CellBaseR-method	0.074	0.000	2.787
getTfbsByRegion	0.087	0.000	0.597
getTranscript-CellBaseR-method	0.065	0.000	0.548
getTranscriptByGene	0.065	0.000	0.548
getVariant-CellBaseR-method	0.156	0.000	0.791
getVariantAnnotation	0.15	0.00	0.77
getXref-CellBaseR-method	0.062	0.000	0.537