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CHECK report for cellbaseR on merida1

This page was generated on 2020-04-15 12:45:21 -0400 (Wed, 15 Apr 2020).

Package 239/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.10.0
Mohammed OE Abdallah
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: RELEASE_3_10
Last Commit: 3cf038b
Last Changed Date: 2019-10-29 13:10:25 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

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

Command output

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### Running 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
###
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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.


Installation output

cellbaseR.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output


Example timings

cellbaseR.Rcheck/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method5.3081.1988.330
CellBaseParam0.0040.0010.004
CellBaseR0.0430.0050.346
createGeneModel0.1870.0230.854
getCaddScores0.0570.0060.566
getCellBase-CellBaseR-method0.0590.0060.578
getCellBaseResourceHelp0.2400.0320.866
getChromosomeInfo-CellBaseR-method0.0570.0050.560
getClinical-CellBaseR-method0.7600.0291.749
getClinicalByRegion1.6980.0553.168
getConservationByRegion0.0880.0050.758
getGene-CellBaseR-method0.1320.0040.786
getGeneInfo0.0570.0030.576
getMeta-CellBaseR-method0.0730.0030.581
getProtein-CellBaseR-method0.1360.0050.747
getProteinInfo0.1430.0030.753
getRegion-CellBaseR-method0.1310.0040.885
getRegulatoryByRegion0.1320.0051.063
getSnp-CellBaseR-method0.0620.0030.596
getSnpByGene0.0690.0020.607