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This page was generated on 2023-03-31 11:03:15 -0400 (Fri, 31 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4308
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

BUILD results for ORFik on palomino3


To the developers/maintainers of the ORFik package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ORFik.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1427/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.19.8  (landing page)
Haakon Tjeldnes
Snapshot Date: 2023-03-30 14:00:16 -0400 (Thu, 30 Mar 2023)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: devel
git_last_commit: 7d13ceb
git_last_commit_date: 2023-03-23 10:21:25 -0400 (Thu, 23 Mar 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped

Summary

Package: ORFik
Version: 1.19.8
Command: chmod a+r ORFik -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ORFik
StartedAt: 2023-03-30 20:47:11 -0400 (Thu, 30 Mar 2023)
EndedAt: 2023-03-30 20:53:25 -0400 (Thu, 30 Mar 2023)
EllapsedTime: 373.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r ORFik -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ORFik
###
##############################################################################
##############################################################################


* checking for file 'ORFik/DESCRIPTION' ... OK
* preparing 'ORFik':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'Annotation_Alignment.Rmd' using rmarkdown
--- finished re-building 'Annotation_Alignment.Rmd'

--- re-building 'Importing_Data.Rmd' using rmarkdown
Quitting from lines 151-163 (Importing_Data.Rmd) 
Error: processing vignette 'Importing_Data.Rmd' failed with diagnostics:
invalid 'file' argument
--- failed re-building 'Importing_Data.Rmd'

--- re-building 'ORFikExperiment.Rmd' using rmarkdown
--- finished re-building 'ORFikExperiment.Rmd'

--- re-building 'ORFikOverview.Rmd' using rmarkdown
--- finished re-building 'ORFikOverview.Rmd'

--- re-building 'Ribo-seq_pipeline.Rmd' using rmarkdown
--- finished re-building 'Ribo-seq_pipeline.Rmd'

--- re-building 'Working_with_transcripts.Rmd' using rmarkdown
Quitting from lines 29-42 (Working_with_transcripts.Rmd) 
Error: processing vignette 'Working_with_transcripts.Rmd' failed with diagnostics:
invalid 'file' argument
--- failed re-building 'Working_with_transcripts.Rmd'

SUMMARY: processing the following files failed:
  'Importing_Data.Rmd' 'Working_with_transcripts.Rmd'

Error: Vignette re-building failed.
Execution halted