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neurogenomics / EpiCompare

Comparison, benchmarking & QC of epigenetic datasets
https://doi.org/doi:10.18129/B9.bioc.EpiCompare
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`WARNING: The following files are over 5MB in size: 'inst/doc/example_report.html'` #151

Closed bschilder closed 1 year ago

bschilder commented 1 year ago

1. Bug description

I believe this is happening when the vignettes get rendered. Let me see if I can get rid of this by adding vignettes/html to the .Rbuildignore*.

Oddly, doesn't seem to occur locally (on my Mac) during checks. Screenshot 2023-03-08 at 21 05 30

Console output

https://github.com/neurogenomics/EpiCompare/actions/runs/4366324072/jobs/7636174158#step:4:6765

* Checking package size...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* Checking individual file sizes...
    * WARNING: The following files are over 5MB in size:
      'inst/doc/example_report.html'

Expected behaviour

(A clear and concise description of what you expected to happen.)

2. Reproducible example

Code

https://github.com/neurogenomics/EpiCompare/actions/runs/4366324072/workflow

3. Session info

``` ─ Session info ─────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.2.2 (2022-10-31) os macOS Big Sur ... 10.16 system x86_64, darwin17.0 ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz UTC date 2023-03-08 pandoc 2.19.2 @ /usr/local/bin/pandoc ─ Packages ─────────────────────────────────────────────────────────────────────────────────────── ! package * version date (UTC) lib source annotate 1.76.0 2022-11-01 [1] Bioconductor AnnotationDbi 1.60.0 2022-11-01 [1] Bioconductor AnnotationHub 3.6.0 2022-11-01 [1] Bioconductor ape 5.7 2023-02-16 [1] CRAN (R 4.2.0) aplot 0.1.10 2023-03-08 [1] CRAN (R 4.2.2) askpass 1.1 2019-01-13 [1] CRAN (R 4.2.0) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0) badger 0.2.3 2023-01-28 [1] CRAN (R 4.2.0) base * 4.2.2 2022-10-31 [?] local base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0) BH 1.81.0-1 2023-01-22 [1] CRAN (R 4.2.0) Biobase 2.58.0 2022-11-01 [1] Bioconductor BiocFileCache 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bschilder commented 1 year ago

I believe this is happening when the vignettes get rendered. Let me see if I can get rid of this by adding *vignettes/html to the .Rbuildignore.

This didn't seem to help: https://github.com/neurogenomics/EpiCompare/actions/runs/4368536514/jobs/7641247965

We have to change strategies and host the full vignette on another GitHub repo, and only provide the link (and perhaps a download button) in the vignette

bschilder commented 1 year ago

I've now created EpiArchives: a new repo for storing EpiCompare reports: https://github.com/neurogenomics/EpiArchives

I've updated _vignettes/examplereport.Rmd so that it just renders the markdown landing page for EpiArchives.

bschilder commented 1 year ago

Some other random error now, even though this should be super simple. Will resort to copying the markdown content rather than trying to embed the page

pandoc: /EpiArchives/assets/css/style.css: withBinaryFile: does not exist (No such file or directory)
Error: processing vignette 'example_report.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘example_report.Rmd’
SUMMARY: processing the following file failed:
  ‘example_report.Rmd’
Error: Vignette re-building failed.