[Bioc-devel] RforProteomics: vignette error - cannot find the file(s)

Laurent Gatto |@urent@g@tto @end|ng |rom uc|ouv@|n@be
Fri Apr 28 17:36:23 CEST 2023

Yes, that's a very good suggestion indeed, but doesn't look it is the reason

- the .gitignore files contains vignettes/figure, without the s, although I wouldn't know for sure if this would impact the directory (I'll remove it, just it case)
- the figures directory exists on github [1]
- I cloned the repo from git.bioconductor.org and it's also present there (with all the figures)

Thank you anyway!

[1] https://github.com/lgatto/RforProteomics/tree/master/vignettes/figures

From: Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com>
Sent: 28 April 2023 16:53
To: Laurent Gatto
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] RforProteomics: vignette error - cannot find the file(s)

I wonder if it's because the entire "vignettes/figures" is not pushed to Bioc git (it's included in your .gitignore). And the previous chunk does not re-create the figure.


On Fri, 28 Apr 2023 at 15:24, Laurent Gatto <laurent.gatto using uclouvain.be<mailto:laurent.gatto using uclouvain.be>> wrote:
I am puzzled by this error:

The vignette fails because it can't find a figure

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘RProtVis.Rmd’ using rmarkdown
Quitting from lines 607-608 (RProtVis.Rmd)
Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
Cannot find the file(s): "figures/msanim1.gif"
--- failed re-building ‘RProtVis.Rmd’

Even though that figure does exists [1].

I am unable to reproduce locally and on Github [2]

Source: [3]

Any idea?


[1] https://github.com/lgatto/RforProteomics/tree/master/vignettes/figures
[2] If fails at the moment, but for a different reason - a dependency is not (yet?) available
[3] https://master.bioconductor.org/checkResults/3.17/data-experiment-LATEST/RforProteomics/nebbiolo1-checksrc.html

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