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CHECK report for cellbaseR on nebbiolo1

This page was generated on 2020-09-19 10:17:44 -0400 (Sat, 19 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cellbaseR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 241/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.13.0
Mohammed OE Abdallah
Snapshot Date: 2020-09-18 14:43:25 -0400 (Fri, 18 Sep 2020)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: master
Last Commit: e14a517
Last Changed Date: 2020-04-27 15:07:27 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ ERROR ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  ERROR  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: cellbaseR
Version: 1.13.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cellbaseR_1.13.0.tar.gz
StartedAt: 2020-09-18 21:43:48 -0400 (Fri, 18 Sep 2020)
EndedAt: 2020-09-18 21:45:51 -0400 (Fri, 18 Sep 2020)
EllapsedTime: 123.1 seconds
RetCode: 1
Status:  ERROR 
CheckDir: cellbaseR.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cellbaseR_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/cellbaseR.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.13.0’
* 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: getConservationByRegion
> ### Title: getConservationByRegion
> ### Aliases: getConservationByRegion
> 
> ### ** Examples
> 
> cb <- CellBaseR()
> res <- getConservationByRegion(cb, "17:1000000-1189811")
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: getConservationByRegion ... 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/cellbaseR.Rcheck/00check.log’
for details.


Installation output

cellbaseR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL cellbaseR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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)

Tests output


Example timings

cellbaseR.Rcheck/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method3.5960.8938.709
CellBaseParam0.0000.0020.002
CellBaseR0.0270.0080.319
createGeneModel0.1790.0040.950
getCaddScores0.0490.0040.533
getCellBase-CellBaseR-method0.0660.0000.541
getCellBaseResourceHelp0.1840.0280.779
getChromosomeInfo-CellBaseR-method0.0490.0080.523
getClinical-CellBaseR-method1.3830.0762.492
getClinicalByRegion0.8680.0122.930