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Bioconductor packages need to be re-detected for installation #365
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Honestly, I am so dang embarrassed about this |
I belive the problem is coming from the fact that |
Note, that the above function is called in the cascade from |
N.B. the error is coming from Lines 256 to 259 in d94acec
|
N.B. I found that this is a bootstrapping problem. If we use a pattern like: library(sandpaper)
manage_deps()
done <- work_with_cache()
renv::install("bioc::SummarizedExperiment")
renv::install("bioc::tidySummarizedExperiment")
done()
manage_deps() Then things install correctly, so I might be able to catch those and try them with |
This provides a second chance to install bioconductor packages that were missed on the first pass by implementing the strategy in <#365 (comment)>, which is to prepend the package name with `bioc::` and re-run `renv::install()`
Note that |
In the transformation of https://github.com/carpentries-incubator/bioc-intro in https://github.com/fishtree-attempt/bioc-intro:
Solution
I believe the solution is to include
bioconductor = TRUE
insandpaper/R/utils-renv.R
Line 132 in d94acec
That being said, I will have to see if that's going to affect non-bioconductor lessons.
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