[traine@login01.caviness ~]$ workgroup -g it_css
[(it_css:traine)@login01.caviness ~]$ vpkg_devrequire r/4.1 gdal/3.4.3 geos/3.9.1
Adding dependency `binutils/2.35` to your environment
Adding dependency `gcc/11.2.0` to your environment
Adding dependency `atlas/3.10.3` to your environment
Adding package `r/4.1.3` to your environment
Adding dependency `szip/2.1.1` to your environment
Adding dependency `hdf4/4.2.13` to your environment
Adding dependency `hdf5/1.10.2` to your environment
Adding dependency `netcdf/4.6.1` to your environment
Adding dependency `sqlite3/3.34.1` to your environment
Adding dependency `proj/8.2.1` to your environment
Adding package `gdal/3.4.3` to your environment
Adding package `geos/3.9.1` to your environment
[(it_css:traine)@login01.caviness ~]$ echo $LDFLAGS
-L/opt/shared/binutils/2.35/lib -L/opt/shared/gcc/11.2.0/lib -L/opt/shared/gcc/11.2.0/lib64 -L/opt/shared/atlas/30.3/lib -L/opt/shared/r/4.1.3/lib64 -L/opt/shared/r/4.1.3/lib64/R/lib -L/opt/shared/r/4.1.3/lib64/R/lib/atlas -L/t/shared/szip/2.1.1/lib -L/opt/shared/hdf4/4.2.13/lib -L/opt/shared/hdf5/1.10.2/lib -L/opt/shared/netcdf/4.6.1/li-L/opt/shared/sqlite3/3.34.1/lib -L/opt/shared/proj/8.2.1/lib -L/opt/shared/gdal/3.4.3/lib -L/opt/shared/geos/3.9/lib
[(it_css:traine)@login01.caviness ~]$ echo $CPPFLAGS
-I/opt/shared/binutils/2.35/include -I/opt/shared/gcc/11.2.0/include -I/opt/shared/atlas/3.10.3/include -I/opt/shared/r/4.1.3/include -I/opt/shared/r/4.1.3/lib64/R/include -I/opt/shared/szip/2.1.1/include -I/opt/shared/hdf4/4.2.13/include -I/opt/shared/hdf5/1.10.2/include -I/opt/shared/netcdf/4.6.1/include -I/opt/shared/sqlite3/3.34.1/include -I/opt/shared/proj/8.2.1/include -I/opt/shared/gdal/3.4.3/include -I/opt/shared/geos/3.9.1/include
[(it_css:traine)@login01.caviness ~]$ echo $LIBRARY_PATH
/opt/shared/geos/3.9.1/lib:/opt/shared/gdal/3.4.3/lib:/opt/shared/proj/8.2.1/lib:/opt/shared/sqlite3/3.34.1/lib:/opt/shared/netcdf/4.6.1/lib:/opt/shared/hdf5/1.10.2/lib:/opt/shared/hdf4/4.2.13/lib:/opt/shared/szip/2.1.1/lib:/opt/shared/r/4.1.3/lib64/R/lib/atlas:/opt/shared/r/4.1.3/lib64/R/lib:/opt/shared/r/4.1.3/lib64:/opt/shared/atlas/3.10.3/lib:/opt/shared/gcc/11.2.0/lib64:/opt/shared/gcc/11.2.0/lib:/opt/shared/binutils/2.35/lib
[(it_css:traine)@login01.caviness ~]$ echo $LD_LIBRARY_PATH
/opt/shared/geos/3.9.1/lib:/opt/shared/gdal/3.4.3/lib:/opt/shared/proj/8.2.1/lib:/opt/shared/sqlite3/3.34.1/lib:/opt/shared/netcdf/4.6.1/lib:/opt/shared/hdf5/1.10.2/lib:/opt/shared/hdf4/4.2.13/lib:/opt/shared/szip/2.1.1/lib:/opt/shared/r/4.1.3/lib64/R/lib/atlas:/opt/shared/r/4.1.3/lib64/R/lib:/opt/shared/r/4.1.3/lib64:/opt/shared/atlas/3.10.3/lib:/opt/shared/gcc/11.2.0/lib64:/opt/shared/gcc/11.2.0/lib:/opt/shared/binutils/2.35/lib:/opt/shared/slurm/lib
[(it_css:traine)@login01.caviness ~]$ env | grep PREFIX
R_PREFIX=/opt/shared/r/4.1.3
GDAL_PREFIX=/opt/shared/gdal/3.4.3
GCC_PREFIX=/opt/shared/gcc/11.2.0
GEOS_PREFIX=/opt/shared/geos/3.9.1
HDF5_PREFIX=/opt/shared/hdf5/1.10.2
SQLITE3_PREFIX=/opt/shared/sqlite3/3.34.1
PROJ_PREFIX=/opt/shared/proj/8.2.1
NETCDF_PREFIX=/opt/shared/netcdf/4.6.1
GQUEUE_PREFIX=/opt/shared/gqueue
HDF4_PREFIX=/opt/shared/hdf4/4.2.13
BINUTILS_PREFIX=/opt/shared/binutils/2.35
SZIP_PREFIX=/opt/shared/szip/2.1.1
ATLAS_PREFIX=/opt/shared/atlas/3.10.3
[(it_css:traine)@login01.caviness ~]$ mkdir -p $WORKDIR/sw/r/add-ons/r4.1.3/terra
[(it_css:traine)@login01.caviness ~]$ export R_LIBS="$WORKDIR/sw/r/add-ons/r4.1.3/terra"
[(it_css:traine)@login01.caviness ~]$ R -q --no-save
> .libPaths()
[1] "/work/it_css/sw/r/add-ons/r4.1.3/terra"
[2] "/opt/shared/r/4.1.3/lib64/R/library"
> chooseCRANmirror(all)
Secure CRAN mirrors

 1: 0-Cloud [https]
 2: Australia (Canberra) [https]
 3: Australia (Melbourne 1) [https]
 4: Australia (Melbourne 2) [https]
 5: Australia (Perth) [https]
 6: Austria [https]
 ...
69: USA (IA) [https]
70: USA (MI) [https]
71: USA (MO) [https]
72: USA (OH) [https]
73: USA (OR) [https]
74: USA (TN) [https]
75: United Arab Emirates [https]
76: Uruguay [https]
77: (other mirrors)

Selection: 69
> install.packages("quantregForest", dependencies=TRUE)
Installing package into ‘/work/it_css/sw/r/add-ons/r4.1.3/terra’
(as ‘lib’ is unspecified)
also installing the dependencies ‘fs’, ‘R6’, ‘rappdirs’, ‘base64enc’, ‘cachem’, ‘lifecycle’, ‘memoise’, ‘mime’, ‘rlang’, ‘sass’, ‘digest’, ‘ellipsis’, ‘fastmap’, ‘cli’, ‘glue’, ‘magrittr’, ‘stringi’, ‘vctrs’, ‘evaluate’, ‘highr’, ‘xfun’, ‘yaml’, ‘bslib’, ‘fontawesome’, ‘htmltools’, ‘jquerylib’, ‘jsonlite’, ‘stringr’, ‘tinytex’, ‘randomForest’, ‘RColorBrewer’, ‘gss’, ‘knitr’, ‘rmarkdown’

trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/fs_1.6.3.tar.gz'
Content type 'application/x-gzip' length 1185603 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
...
...
...
ERROR: dependency ‘bslib’ is not available for package ‘rmarkdown’
* removing ‘/work/it_css/sw/r/add-ons/r4.1.3/terra/rmarkdown’

The downloaded source packages are in
        ‘/tmp/RtmpaBulVZ/downloaded_packages’
Warning message:
In install.packages("quantregForest", dependencies = TRUE) :
  installation of package ‘rmarkdown’ had non-zero exit status
> library (quantregForest)
Loading required package: randomForest
randomForest 4.7-1.1
Type rfNews() to see new features/changes/bug fixes.
Loading required package: RColorBrewer
> install.packages("bslib", dependencies=TRUE)
Installing package into ‘/work/it_css/sw/r/add-ons/r4.1.3/terra’
(as ‘lib’ is unspecified)
also installing the dependencies ‘colorspace’, ‘utf8’, ‘prettyunits’, ‘labeling’, ‘munsell’, ‘viridisLite’, ‘fansi’, ‘pillar’, ‘pkgconfig’, ‘Rcpp’, ‘rprojroot’, ‘pkgbuild’, ‘diffobj’, ‘rematch2’, ‘gtable’, ‘isoband’, ‘scales’, ‘tibble’, ‘httpuv’, ‘xtable’, ‘sourcetools’, ‘later’, ‘promises’, ‘crayon’, ‘commonmark’, ‘brio’, ‘callr’, ‘desc’, ‘pkgload’, ‘praise’, ‘processx’, ‘ps’, ‘waldo’, ‘farver’, ‘rstudioapi’, ‘bsicons’, ‘curl’, ‘ggplot2’, ‘rmarkdown’, ‘shiny’, ‘testthat’, ‘thematic’, ‘withr’
...
...
checking for udunits2.h... no
checking for udunits2/udunits2.h... no
checking for ut_read_xml in -ludunits2... yes
configure: error: in `/tmp/Rtmpc5hPQz/R.INSTALL540e8c2492d/units':
configure: error:
--------------------------------------------------------------------------------
  Configuration failed because udunits2.h 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.
--------------------------------------------------------------------------------

See `config.log' for more details
ERROR: configuration failed for package ‘units’
* removing ‘/work/it_css/sw/r/add-ons/r4.1.3/terra/units’

The downloaded source packages are in
        ‘/tmp/Rtmps25MZ6/downloaded_packages’
Warning message:
In install.packages("units", dependencies = TRUE) :
  installation of package ‘units’ had non-zero exit status
> quit()
[(it_css:traine)@login01.caviness ~]$ vpkg_devrequire udunits/2.2
Adding package `udunits/2.2.26` to your environment
[(it_css:traine)@login01.caviness ~]$ env | grep UDUNITS
UDUNITS_PREFIX=/opt/shared/udunits/2.2.26
[(it_css:traine)@login01.caviness ~]$ export UDUNITS2_INCLUDE=$UDUNITS_PREFIX/include
[(it_css:traine)@login01.caviness ~]$ export UDUNITS2_LIBS=$UDUNITS_PREFIX/lib
[(it_css:traine)@login01.caviness ~]$ R -q --no-save
> .libPaths()
[1] "/work/it_css/sw/r/add-ons/r4.1.3/terra"
[2] "/opt/shared/r/4.1.3/lib64/R/library"
> chooseCRANmirror(all)
Secure CRAN mirrors

 1: 0-Cloud [https]
 2: Australia (Canberra) [https]
 3: Australia (Melbourne 1) [https]
 4: Australia (Melbourne 2) [https]
 5: Australia (Perth) [https]
 6: Austria [https]
...
...
69: USA (IA) [https]
70: USA (MI) [https]
71: USA (MO) [https]
72: USA (OH) [https]
73: USA (OR) [https]
74: USA (TN) [https]
75: United Arab Emirates [https]
76: Uruguay [https]
77: (other mirrors)

Selection: 69
> install.packages("units", dependencies=TRUE)
Installing package into ‘/work/it_css/sw/r/add-ons/r4.1.3/terra’
(as ‘lib’ is unspecified)
trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/units_0.8-4.tar.gz'
Content type 'application/x-gzip' length 248024 bytes (242 KB)
==================================================
downloaded 242 KB

* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 0.8-4
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether /opt/shared/gcc/11.2.0/bin/g++ -std=gnu++14 accepts -g... yes
checking for /opt/shared/gcc/11.2.0/bin/g++ -std=gnu++14 option to enable C++11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for _Bool... no
checking for stdbool.h that conforms to C99... yes
checking for error_at_line... yes
checking for gcc... /opt/shared/gcc/11.2.0/bin/gcc
checking whether the compiler supports GNU C... yes
checking whether /opt/shared/gcc/11.2.0/bin/gcc accepts -g... yes
checking for /opt/shared/gcc/11.2.0/bin/gcc option to enable C11 features... none needed
checking for XML_ParserCreate in -lexpat... yes
checking for udunits2.h... yes
checking for ut_read_xml in -ludunits2... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
/opt/shared/gcc/11.2.0/bin/g++ -std=gnu++14 -I"/opt/shared/r/4.1.3/lib64/R/include" -DNDEBUG -DUDUNITS2_DIR=0 -I/opt/shared/udunits/2.2.26/include -I/opt/shared/udunits/2.2.26/include -I/opt/shared/binutils/2.35/include -I/opt/shared/gcc/11.2.0/include -I/opt/shared/r/4.1.3/include -I'/work/it_css/sw/r/add-ons/r4.1.3/terra/Rcpp/include' -I/opt/shared/binutils/2.35/include -I/opt/shared/gcc/11.2.0/include -I/opt/shared/r/4.1.3/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
/opt/shared/gcc/11.2.0/bin/g++ -std=gnu++14 -I"/opt/shared/r/4.1.3/lib64/R/include" -DNDEBUG -DUDUNITS2_DIR=0 -I/opt/shared/udunits/2.2.26/include -I/opt/shared/udunits/2.2.26/include -I/opt/shared/binutils/2.35/include -I/opt/shared/gcc/11.2.0/include -I/opt/shared/r/4.1.3/include -I'/work/it_css/sw/r/add-ons/r4.1.3/terra/Rcpp/include' -I/opt/shared/binutils/2.35/include -I/opt/shared/gcc/11.2.0/include -I/opt/shared/r/4.1.3/include   -fpic  -g -O2  -c udunits.cpp -o udunits.o
/opt/shared/gcc/11.2.0/bin/g++ -std=gnu++14 -shared -L/opt/shared/r/4.1.3/lib64/R/lib -L/opt/shared/binutils/2.35/lib -L/opt/shared/gcc/11.2.0/lib -L/opt/shared/gcc/11.2.0/lib64 -I/opt/shared/r/4.1.3/lib64 -o units.so RcppExports.o udunits.o -lexpat -L/opt/shared/udunits/2.2.26/lib -lexpat -ludunits2 -L/opt/shared/r/4.1.3/lib64/R/lib -lR
installing to /work/it_css/sw/r/add-ons/r4.1.3/terra/00LOCK-units/00new/units/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (units)
> library(terra)
terra 1.7.55
> library(quantregForest)
Loading required package: randomForest
randomForest 4.7-1.1
Type rfNews() to see new features/changes/bug fixes.
Loading required package: RColorBrewer
> quit()
[(it_css:traine)@login01.caviness ~]$