EdgeR cannot be updated

Question

[thomas.heigl]

Hi all

I tried to update EdgeR since I wanted to begin a new project with a complete update there. After updating BiocManager, I wasn't able to update EdgeR.

See code and output below. Somehow it cannot reach a repository. Any suggestion how to proceed? For a similar problem from 2021 there was a quick fix for that specific BiocManager version. But for this one I don't know how to proceed.

Thank you.

BiocManager::install("edgeR")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for
details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Warning: cannot open URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES.rds': HTTP status was '404 Not Found'Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'edgeR'Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, cluster, Matrix, mgcv, nlme, rpart, spatial

packageVersion("edgeR")
[1] ‘3.42.4’

sessionInfo( )
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=de_CH.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=de_CH.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=de_CH.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Zurich
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.3.2      tools_4.3.2         rstudioapi_0.15.0   knitr_1.45          xfun_0.41

[thomas.heigl]

I am sorry I needed to post this here. On the Bioconductor forum I cannot post anything and I do not know why. Due to my visual impairment I also do not see any hints be color or with a bad contrast. But apparently this issue is known as I have read on the github page but still occuring.

Thank you.

Answer 1

[Dave Carlson]

The problem appears to be indicated with the following:

'edgeR'Installation paths not writeable, unable to update packages

It looks like you are installing packages to /usr/lib/R/library, which is not user writeable by default.

You could do the following:

1. If you have sudo/root access, change the permissions for the above directory so that it's writeable for regular users. This is probably not a good idea for security reasons
2. Change the location where libraries are installed to somewhere you already have write permission to. This is probably the better option. There are several ways to do this, some of which are discussed here.

[Ram]

That's the third thing - the first is the inability to access the URL and the second is the message about the latest version already being installed. Are you sure the permission error is the reason OP's unable to update?

[Dave Carlson]

Not certain, no. But the inability to write to the package library directory can cause package install failures, and the other two issues are warnings. So I would bet that the permissions are the primary culprit, but I could be wrong.