`Installation paths not writeable, unable to update packages` under certain Linux setups

[multimeric]

I support a research organisation that provides R on a shared HPC system. We sporadically encounter researchers seeing this R error and being confused:

Installation paths not writeable, unable to update packages

In some cases this happens even when the package does install correctly, which makes the message even more confusing. I've dug into this problem and been able to identify a minimal reproducible example. This happen when you have a writeable library (ie a user library), and a non-writeable library (ie a site library, provided by the HPC admins).

To reproduce, firstly setup an renv that emulates a shared HPC installation of R, e.g.

install.packages("renv")
renv::init()

Then restart R and run:

install.packages("BiocManager")
BiocManager::install("BiocVersion")

You will likely get the following output:

# Installing packages --------------------------------------------------------
- Installing BiocManager ...                    OK [linked from cache]
Successfully installed 1 package in 45 milliseconds.
> BiocManager::install("BiocVersion")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://packagemanager.posit.co/cran/__linux__/rhel9/latest
Bioconductor version 3.22 (BiocManager 1.30.27), R 4.5.2 (2025-10-31)
Installing package(s) 'BiocVersion'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/BiocVersion_3.22.0.tar.gz'
Content type 'application/x-gzip' length 1112 bytes
==================================================
downloaded 1112 bytes

* installing *source* package ‘BiocVersion’ ...
** this is package ‘BiocVersion’ version ‘3.22.0’
** package ‘BiocVersion’ successfully unpacked and MD5 sums checked
** using staged installation
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocVersion)

The downloaded source packages are in
        ‘/XXX/RtmpOM95W8/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /XXX/cache/R/renv/sandbox/linux-rhel-9.3/R-4.5/x86_64-pc-linux-gnu/cae5638a
  packages:
    mgcv, survival
Old packages: 'renv'
Update all/some/none? [a/s/n]: n

Note how BiocVersion did successfully install, but we still get Installation paths not writeable, unable to update packages.

This replicates my HPC issue because renv uses a "sandbox" which is read only, so this will trigger our error.

It would be great if we could avoid this confusing error.

[LiNk-NY]

Hi @multimeric
Thank you for the issue. I wasn't able to reproduce this on Ubuntu 24.04 LTE.
In any event, we don't really recommend the use of renv because BiocManager already tightly controls the versioning of Bioconductor packages (using the latest versions of CRAN). If you wish to use previous Bioconductor releases alongside previous CRAN snapshots, I recommend using @Bioconductor/BiocArchive to obtain the contemporary versions of CRAN packages.

The message can be ignored as there is not much BiocManager can do with packages that mangle the .libPaths().

[multimeric]

That's odd, I just reproduced it on Ubuntu 22.04:

* DONE (BiocVersion)

The downloaded source packages are in
	‘/tmp/RtmpaaEicQ/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /home/migwell/.cache/R/renv/sandbox/linux-pop-jammy/R-4.5/x86_64-pc-linux-gnu/9a444a72
  packages:
    codetools, lattice, spatial, survival

In any case, the issue is not about renv, this was just a way to easily reproduce the problem. The issue is about HPC facilities and maybe all Linux environments where the site library is non-writeable by regular users. For example on Ubuntu 22.04 without renv, simply installing BiocVersion causes:

Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library

The message can be ignored

The message causes confusion in users who think BioC packages have not successfully installed, especially since it comes after any successful looking messages. For this reason I think it would be great to omit it when it provides no useful information.