R Packages and System Modules
- Simon Alexander
Owned by Simon Alexander
Goal: Installing some R packages requires understanding what libraries are available on the System.
Start a new Session and Start R
[]$ module purge
[]$ module load gcc/13.2.0 r/4.4.0
[]$ R
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
...Try Installing R XML Package
> install.packages("XML")
...
checking for xml2-config... /apps/u/spack/gcc/13.2.0/libxml2/2.10.3-5toq4pi/bin/xml2-config
...
Located parser file -I/apps/u/spack/gcc/13.2.0/libxml2/2.10.3-5toq4pi/include/libxml2 -I/apps/u/spack/gcc/13.2.0/libiconv/1.17-3dj22ny/include/parser.h
Checking for 1.8: -I/apps/u/spack/gcc/13.2.0/libxml2/2.10.3-5toq4pi/include/libxml2 -I/apps/u/spack/gcc/13.2.0/libiconv/1.17-3dj22ny/include
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... yes
You are trying to use a version 2.* edition of libxml but an incompatible library. The header files and library seem to be
mismatched. If you have specified LIBXML_INCDIR, make certain to also specify an appropriate LIBXML_LIBDIR if the
libxml2 library is not in the default directories.
ERROR: configuration failed for package ‘XML’
* removing ‘/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4/XML’
...What does the error message mean?
How to Resolve XML Package Issue
We can see from the CRAN package XML description that from the System Requirements we require: libxml2 (>= 2.6.3)
We can see that the libxml2 library is available and is being picked up.
[]$ ml
Currently Loaded Modules:
...
15) libxml2/2.10.3 56) nghttp2/1.57.0
...Install location: /apps/u/spack/gcc/13.2.0/libxml2/2.10.3-5toq4pi
Install the R sf Package
Install the R sf Package: Fails
Do we have a udunits module?