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Start a new Session and Start R
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[salexan5@mblog2 ~]$ module purge []$ module load gcc/13.2.0 r/4.4.0 [salexan5@mblog2 ~]$ R R version 4.4.0 (2024-04-24) -- "Puppy Cup" ... |
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> install.packages("XML")
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checking for xml2-config... /apps/u/spack/gcc/13.2.0/libxml2/2.10.3-5toq4pi/bin/xml2-config
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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/salexan5<username>/R/x86_64-pc-linux-gnu-library/4.4/XML’
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We can see that the
Install location: |
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Reading the CRAN sf definition page, take note of the system requirements: System Requirements: GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0), sqlite3 What do we already have loaded? |
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[salexan5@mblog2 ~]$ ml
Currently Loaded Modules:
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35) sqlite/3.43.2 76) scrnsaverproto/1.2.2
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We also need to manually load:
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Do we have a udunits module?
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[powersw@mblog2 ~]$ module spider udunits
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udunits: udunits/2.2.28
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You will need to load all module(s) on any one of the lines below before the "udunits/2.2.28" module is available to load.
arcc/1.0 gcc/13.2.0
Help:
Automated units conversion |
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[powersw@mblog2 ~]$ module load udunits/2.2.28
# Within R
> install.packages("sf")
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* DONE (sf)
> library(sf)
Linking to GEOS 3.12.0, GDAL 3.7.3, PROJ 9.2.1; sf_use_s2() is TRUE |
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Recommendation: When ever you want to use this R package, additionally load:
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