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From https://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder/nebbiolo1-buildsrc.html ``` * creating vignettes ... ERROR --- re-building ‘derfinder-quickstart.Rmd’ using rmarkdown Quitting from lines 343-378 (derfinder-quickstart.Rmd) Error: processing vignette 'derfinder-quickstart.Rmd' failed with diagnostics: subscript out of bounds --- failed re-building ‘derfinder-quickstart.Rmd’ --- re-building ‘derfinder-users-guide.Rmd’ using rmarkdown Warning in in_dir(input_dir(), expr) : You changed the working directory to /tmp/RtmphAsNWX/Rbuild4c29c999c132/derfinder/vignettes/analysisResults (probably via setwd()). It will be restored to /tmp/RtmphAsNWX/Rbuild4c29c999c132/derfinder/vignettes. See the Note section in ?knitr::knit Quitting from lines 1341-1459 (derfinder-users-guide.Rmd) Error: processing vignette 'derfinder-users-guide.Rmd' failed with diagnostics: subscript out of bounds --- failed re-building ‘derfinder-users-guide.Rmd’ SUMMARY: processing the following files failed: ‘derfinder-quickstart.Rmd’ ‘derfinder-users-guide.Rmd’ Error: Vignette re-building failed. Execution halted ``` It turns out that `citation("derfinderHelper")` has a length of 2. So it automatically creates two entries in the `bib` object: `bib[['derfinderHelper1']]` and `bib[['derfinderHelper2']]`. Thus `bib[['derfinderHelper']]` is not found later on, and this leads to the subscript out of bounds.
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