Goal: Installing some R packages requires understanding what libraries are available on the System.
...
Start a new Session and Start R
| Code Block |
|---|
[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" ... |
...
| Code Block |
|---|
> 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/salexan5<username>/R/x86_64-pc-linux-gnu-library/4.4/XML’
... |
...
How to Resolve XML Package Issue
| Info |
|---|
We can see from the CRAM CRAN package XML description that from the System Requirements we require: |
| Info | ||
|---|---|---|
We can see that the
Install location: |
...
| Info |
|---|
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? |
| Code Block |
|---|
[salexan5@mblog2 ~]$ ml
Currently Loaded Modules:
...
35) sqlite/3.43.2 76) scrnsaverproto/1.2.2
... |
| Info | ||
|---|---|---|
We also need to manually load:
|
...
Install the R sf Package:
...
Fails
| Code Block |
|---|
> install.packages("sf")
...
also installing the dependencies ‘proxy’, ‘MASS’, ‘e1071’, ‘class’, ‘KernSmooth’, ‘wk’, ‘classInt’, ‘DBI’, ‘Rcpp’, ‘s2’, ‘units’
...
--------------------------------------------------------------------------------
Configuration failed because libudunits2.so was not found. Try installing:
* deb: libudunits2-dev (Debian, Ubuntu, ...)
* rpm: udunits2-devel (Fedora, EPEL, ...)
* brew: udunits (OSX)
If udunits2 is already installed in a non-standard location, use:
--configure-args='--with-udunits2-lib=/usr/local/lib'
if the library was not found, and/or:
--configure-args='--with-udunits2-include=/usr/include/udunits2'
if the header was not found, replacing paths with appropriate values.
You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.
--------------------------------------------------------------------------------
ERROR: configuration failed for package ‘units’
... |
...
Do we have a udunits module?
| Code Block |
|---|
[powersw@mblog2 ~]$ module spider udunits
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
udunits: udunits/2.2.28
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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 |
| Code Block |
|---|
[powersw@mblog2 ~]$ module load udunits/2.2.28 # Within R > install.packages("sf") ... * DONE (sf) > library(sf) Linking to GEOS 3.12.0, GDAL 3.7.3, PROJ 9.2.1; sf_use_s2() is TRUE |
| Info | ||
|---|---|---|
Recommendation: When ever you want to use this R package, additionally load:
|
...
previous section
...
next section
...
...
Prev | Workshop Home | Next |