BioC 3.5: CHECK report for cellbaseR on malbec2

Package: cellbaseR

Version: 1.0.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cellbaseR_1.0.1.tar.gz

StartedAt: 2017-10-17 21:48:24 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:26:13 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 2268.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: cellbaseR.Rcheck

Warnings: NA

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###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cellbaseR_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/cellbaseR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.0.1’
* 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 ... ERROR
Running examples in ‘cellbaseR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getClinicalByGene
> ### Title: getClinicalByGene
> ### Aliases: getClinicalByGene
> 
> ### ** Examples
> 
> cb <- CellBaseR()
> res <- getClinicalByGene(cb, "TET1")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
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Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
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See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Warning: 'rbind.pages' is deprecated.
Use 'rbind_pages' instead.
See help("Deprecated")
Error: all(vapply(pages, is.data.frame, logical(1))) is not TRUE
Execution halted
* 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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/cellbaseR.Rcheck/00check.log’
for details.

* 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	3.376	0.360	15.810
CellBaseParam	0.000	0.000	0.002
CellBaseR	0.216	0.016	0.491
createGeneModel	0.776	0.008	1.373
getCaddScores	0.308	0.000	0.749
getCellBase-CellBaseR-method	0.212	0.000	0.678
getCellBaseResourceHelp	0.496	0.000	1.030
getChromosomeInfo-CellBaseR-method	0.324	0.000	0.770
getClinical-CellBaseR-method	10.996	0.032	12.661