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phenoscape / rphenoscape

R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R.
https://rphenoscape.phenoscape.org/
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Fix error when building vignette #223

Closed johnbradley closed 3 years ago

johnbradley commented 3 years ago

Building the rphenoscape.Rmd vignette recently started failing with an error: 

E> Quitting from lines 37-38 (rphenoscape.Rmd) 
E> Error: processing vignette 'rphenoscape.Rmd' failed with diagnostics:
E> transfer closed with 58771 bytes remaining to read

https://github.com/phenoscape/rphenoscape/blob/0f509b6686201dd2615fb15175da2fc42662491d/vignettes/rphenoscape.Rmd#L36-L38 Running the above line in RStudio works fine (does not produce any error). I first noticed this issue locally running on my laptop. I was able to reproduce the error building the vignette on both the master branch and baseline-v0.3.0. I re-ran an old github action that previously succeeded. It failed there as well with the same error: https://github.com/phenoscape/rphenoscape/runs/2972463875?check_suite_focus=true

johnbradley commented 3 years ago

I am no longer able to reproduce this error. I think this problem was due to some infrastructure problems with the kb.phenoscape.org API that have been resolved.