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allow BioConductor packages to be detected #397

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Feb 14, 2023
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@zkamvar zkamvar commented Feb 14, 2023

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().

Here's an example using the a4Core package (literally the first small package I could find in BioConductor)

> writeLines("library(a4Core)", "episodes/test.R")                                                                                                                            

> sandpaper::manage_deps()                                                                                                                                                    
ℹ Consent to use package cache providedSearching for and installing available dependencies
Done!ng R package dependencies ... 
Done!covering package dependencies ... 
* Copying packages into the cache ... Done!
* Resolving missing dependencies  ... 
The following package(s) were not installed successfully:

	[a4Core]: package 'a4Core' is not available

You may need to manually download and install these packages.

! Attempting to install missing packages assuming bioc
Installing BiocManager [1.30.19] ...
-       OK [linked cache]
Installing BiocGenerics [0.44.0] ...
	OK [linked cache]
Installing Biobase [2.58.0] ...
/       OK [linked cache]
Installing iterators [1.0.14] ...
\       OK [linked cache]
Installing foreach [1.5.2] ...
	OK [linked cache]
Installing shape [1.4.6] ...
	OK [linked cache]
Installing survival [3.5-3] ...
	OK [linked cache]
Installing Rcpp [1.0.10] ...
|       OK [linked cache]
Installing RcppEigen [0.3.3.9.3] ...
-       OK [linked cache]
Installing glmnet [4.1-6] ...
|       OK [linked cache]
Installing a4Core [1.46.0] ...
-       OK [linked cache]
→ Restoring any dependency versions
* The library is already synchronized with the lockfile.Recording changes in lockfile
The following package(s) will be updated in the lockfile:

# Bioconductor =======================
- Biobase        [* -> 2.58.0]
- BiocGenerics   [* -> 0.44.0]
- a4Core         [* -> 1.46.0]

# CRAN ===============================
- BiocManager    [* -> 1.30.19]
- Matrix         [* -> 1.5-3]
- Rcpp           [* -> 1.0.10]
- codetools      [* -> 0.2-19]
- glmnet         [* -> 4.1-6]
- lattice        [* -> 0.20-45]
- shape          [* -> 1.4.6]
- survival       [* -> 3.5-3]

# RSPM ===============================
- RcppEigen      [* -> 0.3.3.9.3]
- foreach        [* -> 1.5.2]
- iterators      [* -> 1.0.14]

* Lockfile written to '/tmp/Rtmp1qs2zv/file2e86154489848/renv/profiles/lesson-requirements/renv.lock'.

I've also tested this locally on other repositories, but I will wait until I do the integration test to release.

This will address #365

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()`
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