Package: cellbaseR

Version: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2020-04-15 01:00:22 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:03:54 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 212.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: cellbaseR.Rcheck

Warnings: NA

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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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/cellbaseR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.0’
* 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 ... ERROR
Running examples in ‘cellbaseR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getTf,CellBaseR-method
> ### Title: getTf
> ### Aliases: getTf,CellBaseR-method getTf
> 
> ### ** Examples
> 
>    cb <- CellBaseR()
>    param <- CellBaseParam(limit = 12)
>    res <- getTf(object=cb, ids="CTCF", resource="tfbs", param=param)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [bioinfo.hpc.cam.ac.uk] Operation timed out after 10001 milliseconds with 0 bytes received
Calls: getTf ... request_fetch -> request_fetch.write_memory -> <Anonymous>
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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/cellbaseR.Rcheck/00check.log’
for details.

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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/3.6/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	5.308	1.198	8.330
CellBaseParam	0.004	0.001	0.004
CellBaseR	0.043	0.005	0.346
createGeneModel	0.187	0.023	0.854
getCaddScores	0.057	0.006	0.566
getCellBase-CellBaseR-method	0.059	0.006	0.578
getCellBaseResourceHelp	0.240	0.032	0.866
getChromosomeInfo-CellBaseR-method	0.057	0.005	0.560
getClinical-CellBaseR-method	0.760	0.029	1.749
getClinicalByRegion	1.698	0.055	3.168
getConservationByRegion	0.088	0.005	0.758
getGene-CellBaseR-method	0.132	0.004	0.786
getGeneInfo	0.057	0.003	0.576
getMeta-CellBaseR-method	0.073	0.003	0.581
getProtein-CellBaseR-method	0.136	0.005	0.747
getProteinInfo	0.143	0.003	0.753
getRegion-CellBaseR-method	0.131	0.004	0.885
getRegulatoryByRegion	0.132	0.005	1.063
getSnp-CellBaseR-method	0.062	0.003	0.596
getSnpByGene	0.069	0.002	0.607