[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 ~]$