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This page was generated on 2021-10-15 15:05:37 -0400 (Fri, 15 Oct 2021).

CHECK results for cellbaseR on nebbiolo1

To the developers/maintainers of the cellbaseR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellbaseR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 258/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.16.0  (landing page)
Mohammed OE Abdallah
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/cellbaseR
git_branch: RELEASE_3_13
git_last_commit: 3bb8377
git_last_commit_date: 2021-05-19 12:27:33 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cellbaseR
Version: 1.16.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cellbaseR_1.16.0.tar.gz
StartedAt: 2021-10-14 09:10:11 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:12:14 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 123.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: cellbaseR.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cellbaseR_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cellbaseR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.16.0’
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/cellbaseR.Rcheck/00check.log’
for details.


Installation output

cellbaseR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cellbaseR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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-method3.9170.9109.820
CellBaseParam0.0000.0020.002
CellBaseR0.0360.0040.344
createGeneModel0.1610.0120.990
getCaddScores0.0470.0040.548
getCellBase-CellBaseR-method0.0520.0080.576
getCellBaseResourceHelp0.1320.0360.768
getChromosomeInfo-CellBaseR-method0.0490.0040.549
getClinical-CellBaseR-method0.4750.0521.639
getClinicalByRegion1.0940.1193.538
getConservationByRegion0.0860.0080.927
getGene-CellBaseR-method0.1500.0070.991
getGeneInfo0.0650.0000.570
getMeta-CellBaseR-method0.0960.0030.598
getProtein-CellBaseR-method0.1520.0000.753
getProteinInfo0.1080.0000.718
getRegion-CellBaseR-method0.1260.0201.066
getRegulatoryByRegion0.1640.0041.145
getSnp-CellBaseR-method0.0740.0040.578
getSnpByGene0.1010.0040.617