BiocManager does not respect `dependencies = TRUE` when the non-Suggests packages have already been installed
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
Research direction
Start by reproducing the two BiocManager::install('phangorn') calls shown in the issue, comparing them with install.packages(..., dependencies = TRUE). Trace the BiocManager::install entry point and dependency-handling path; done means missing dependencies are installed without reinstalling an already current phangorn package.
Written by the indexing model from the issue text.
Description
Reported via email
.libPaths(tempfile())
BiocManager::install('phangorn') # installs phangorn
So far so good, but
> BiocManager::install('phangorn', dependencies = TRUE)
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
(2023-02-21 r83887)
Old packages: 'MASS', 'mgcv', 'survival'
Update all/some/none? [a/s/n]: n
Warning message:
package(s) not installed when version(s) same as or greater than current; use
`force = TRUE` to re-install: 'phangorn'
>
so the dependencies are not installed...
install.packages() says
> install.packages('phangorn', dependencies = TRUE, repos = "https://cran.r-project.org")
Installing package into ‘/private/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T/RtmpsjHQs2’
(as ‘lib’ is unspecified)
Warning: dependencies ‘Biostrings’, ‘seqLogo’ are not available
also installing the dependencies ‘htmlwidgets’, ‘bslib’, ...
It also re-installs 'phangorn', which is not desirable.
I guess a workaround is to follow the BiocManager advice, and install missing dependencies and re-install phangorn.
BiocManager::install('phangorn', dependencies = TRUE, force = TRUE)
> packageVersion('BiocManager')
[1] ‘1.30.20’
- Dominant language
- R
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- 76
- Forks
- 29
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