Fix R dependencies for `renv` migration

[arkid15r]

Context

Some docker images (at least salmon, transcriptome) won't migrate smoothly to renv deps management approach

Problem or idea

The following package(s) were not installed successfully:

    [crancache]: package 'crancache' is not available
    [spp]: package 'spp' is not available
    [preprocessCore]: package 'preprocessCore' is not available
    [EBSeq]: package 'EBSeq' is not available
    [limma]: package 'limma' is not available
    [oligo]: package 'oligo' is not available
    [GenomicRanges]: package 'GenomicRanges' is not available
    [ShortRead]: package 'ShortRead' is not available
    [AnnotationDbi]: package 'AnnotationDbi' is not available
    [tximport]: package 'tximport' is not available

You may need to manually download and install these packages.

The following required packages are not installed:

    codetools  [required by foreach]

Consider reinstalling these packages before snapshotting the lockfile.

Error in snapshot(project = project, library = libpaths, repos = repos,  : 
  aborting snapshot due to pre-flight validation failure
Calls: <Anonymous> -> snapshot
Traceback (most recent calls last):
3: renv::init()
2: snapshot(project = project, library = libpaths, repos = repos, 
       prompt = FALSE)
1: stop("aborting snapshot due to pre-flight validation failure")
Execution halted

Solution or next step

Try installing required packages manually / rebuild docker images.

[arkid15r]

Resolved by installing required versions manually before migration to Bioconductor v3.6