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[package cache] BioConductor lessons need to burn renv down every 6 months #453

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zkamvar opened this issue May 9, 2023 · 0 comments
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bug Something isn't working frequency: low indicator that a use-case has a low-frequency in lessons package cache Related to the {renv} package cache

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@zkamvar
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zkamvar commented May 9, 2023

It turns out that {renv} does not like it when CRAN and BioConductor do not agree on the versions:

from carpentries-incubator/bioc-intro#97 (comment):

  The following Bioconductor packages appear to be from a separate Bioconductor release:
  
  	zlibbioc                 [installed 1.44.0 != latest 1.46.0]
  	tidySummarizedExperiment [installed 1.8.0  != latest 1.10.0]
  	MatrixGenerics           [installed 1.10.0 != latest 1.12.0]
  	S4Vectors                [installed 0.36.1 != latest 0.38.1]
  	GenomicRanges            [installed 1.50.2 != latest 1.52.0]
  	DelayedArray             [installed 0.24.0 != latest 0.26.2]
  	XVector                  [installed 0.38.0 != latest 0.40.0]
  	BiocGenerics             [installed 0.44.0 != latest 0.46.0]
  	IRanges                  [installed 2.32.0 != latest 2.34.0]
  	SummarizedExperiment     [installed 1.28.0 != latest 1.30.1]
  	Biobase                  [installed 2.58.0 != latest 2.60.0]
  	GenomeInfoDb             [installed 1.34.9 != latest 1.36.0]
  
  renv may be unable to restore these packages.
  Bioconductor version: 3.17

The solution at the moment is to delete the renv/ folder and re-run sandpaper::manage_deps()

@zkamvar zkamvar added bug Something isn't working package cache Related to the {renv} package cache frequency: low indicator that a use-case has a low-frequency in lessons labels May 9, 2023
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bug Something isn't working frequency: low indicator that a use-case has a low-frequency in lessons package cache Related to the {renv} package cache
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