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- R 3.4.4
- /usr/lib/R/library
- /usr/lib/R/site-library
- R 3.5.3 – /stor/system/opt/R/R-3.5.3/lib/R/library
- R 3.6.1 – /stor/system/opt/R/R-3.6.1/lib/R/library
Local/Global package installation conflicts
Globally-installed R add-on packages may be updated during system maintenance. This can sometimes cause problems when users invoke R tools with many dependencies (e.g. DESeq2), some of which have been updated system-wide, but others of which have been locally installed and are not at a compatible level. The resulting error messages can be rather obscure, but typically show up after system maintenance has been performed. For example:
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Error in checkSlotAssignment(object, name, value) :
assignment of an object of class “NULL” is not valid for slot ‘NAMES’ in an object of class “DESeqDataSet”; is(value, "characterORNULL") is not TRUE |
To determine if this is due to a local/global package conflict, users can make their local installation directory invisible to R and see if the error goes away like this:
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mv ~/R ~/R.bak |
If this resolves the issue, the user may later find that they need to re-install other packages that were previously installed locally (check the now-named ~/R.bak/x86_64-pc-linux-gnu-library/3.x directory, where x is the R version being used to see locally installed packages).
If this produces a different error indicating that one or more locally installed packages are missing, the user can re-install them then see if the problem is resolved.
Finally, if renaming the local R installation directory does not resolve the issue, it may be an issue with the globally installed packages, so Contact Us.