Bioconductor phyloseq taking forever to install?
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garfield320 ▴ 30
@garfield320-18805
Last seen 21 months ago

I'm trying to install phyloseq package on my computer. I'm using R version 4.0.2 on a 64-bit Windows 10 machine.

I've ran the following lines on Rstudio.

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("phyloseq")


This is what's showing on the console right now:

Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'phyloseq'
also installing the dependencies 'pixmap', 'rhdf5', 'permute', 'ade4', 'biomformat', 'Biostrings', 'igraph', 'multtest', 'reshape2', 'vegan'

There is a binary version available but the source version is later:
binary source needs_compilation


And my Rstudio has been stuck on that screen for several hours now. I've restarted the R session and the computer, then tried to install the ade4 package separately by update.packages() and install.packages("ade4"), but it gets stuck with the same lines. Did anyone else have similar problems when installing phyloseq or really any other Bioconductor packages?

Bioconductor phyloseq • 637 views
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Entering edit mode
@martin-morgan-1513
Last seen 1 day ago
United States

Usually there is a prompt along the lines of 'do you want to install the source version?' and the answer is 'no' (unless the question is 'do you want to install the binary version', and then the answer is 'yes').

I'm not sure why the prompt is not visible to you; perhaps it is an RStudio thing, and you could use the RStudio package manager or install outside R, e.g., in a console.

You can also indicate that you're not interested in installing source packages at all, at least when installing 'ade4', with teh argument type = equal to the appropriate value for binary installations on your (unstated) platform; see the help page ?install.packages for information. It would NOT be a good idea for choosing only binary installations always, because, e.g., Bioconductor annotation packages are only installed as source packages.

It would be interesting to investigate why your work flow does not ask if you would like to install the source or binary package.

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Entering edit mode

I tried installing the package in a console as suggested and it worked. I'm not sure why that prompt wasn't visible either because I haven't had issues with installing other packages in Rstudio (which was also why I thought it might be a Bioconductor issue, but sounds like it isn't). Thank you for your suggestions!