Back to Build/check report for BioC 3.16 annotations
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 06:00:10 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for AHLRBaseDbs on nebbiolo2


To the developers/maintainers of the AHLRBaseDbs package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 3/36HostnameOS / ArchINSTALLBUILDCHECK
AHLRBaseDbs 0.99.3  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2023-04-12 02:30:01 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/AHLRBaseDbs
git_branch: RELEASE_3_16
git_last_commit: c0e6555
git_last_commit_date: 2021-04-21 00:15:17 -0400 (Wed, 21 Apr 2021)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  

Summary

Package: AHLRBaseDbs
Version: 0.99.3
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:AHLRBaseDbs.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings AHLRBaseDbs_0.99.3.tar.gz
StartedAt: 2023-04-12 03:04:31 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 03:05:04 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 32.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: AHLRBaseDbs.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:AHLRBaseDbs.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings AHLRBaseDbs_0.99.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-data-annotation/meat/AHLRBaseDbs.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘AHLRBaseDbs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AHLRBaseDbs’ version ‘0.99.3’
* package encoding: UTF-8
* 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 ‘AHLRBaseDbs’ 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 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 Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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 ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘creating-LRBaseDbs.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘creating-LRBaseDbs.Rmd’ using rmarkdown
Quitting from lines 60-62 (creating-LRBaseDbs.Rmd) 
Error: processing vignette 'creating-LRBaseDbs.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building ‘creating-LRBaseDbs.Rmd’

SUMMARY: processing the following file failed:
  ‘creating-LRBaseDbs.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.16-data-annotation/meat/AHLRBaseDbs.Rcheck/00check.log’
for details.


Installation output

AHLRBaseDbs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL AHLRBaseDbs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘AHLRBaseDbs’ ...
** using staged installation
** inst
** 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 (AHLRBaseDbs)

Tests output


Example timings

AHLRBaseDbs.Rcheck/AHLRBaseDbs-Ex.timings

nameusersystemelapsed
AHLRBaseDbs-package000