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--- technical:recipes:r-in-rlibs [2020-09-05 10:48] – anita
+++ technical:recipes:r-in-rlibs [2020-09-05 12:51] (current) – [VALET Package for R Packages] anita
@@ Line 144: / Line 144: @@
 library(quantregForest)
 install.packages("car", type = "source", configure.args=c('--with-proj-lib=/opt/shared/proj/5.1.0/lib', '--with-proj-include=/opt/shared/proj/5.1.0/include'), dependencies = TRUE)
+install.packages("units", type = "source", configure.args=c('--with-udunits2-lib=/opt/shared/udunits/2.2.26/lib', '--with-udunits2-include=/opt/shared/udunits/2.2.26/include'), dependencies=TRUE)
+library(units)
 install.packages("rgdal", type = "source", configure.args=c('--with-proj-lib=/opt/shared/proj/5.1.0/lib', '--with-proj-include=/opt/shared/proj/5.1.0/include'), dependencies = TRUE)
+library(rgdal)
 install.packages("rasterVis", type = "source", configure.args=c('--with-proj-lib=/opt/shared/proj/5.1.0/lib', '--with-proj-include=/opt/shared/proj/5.1.0/include'), dependencies = TRUE)
 library(rasterVis)
 install.packages("raster", type = "source", configure.args=c('--with-proj-lib=/opt/shared/proj/5.1.0/lib', '--with-proj-include=/opt/shared/proj/5.1.0/include'), dependencies = TRUE)
-install.packages("units", type = "source", configure.args=c('--with-udunits2-lib=/opt/shared/udunits/2.2.26/lib', '--with-udunits2-include=/opt/shared/udunits/2.2.26/include'), dependencies=TRUE)
-library(units)
 install.packages("sf", dependencies = TRUE)
 library(sf)
@@ Line 177: / Line 178: @@
 === Review Installation Output ===
-Review the generated output file, ''install-spatial-09052020.Rout'', for details on each package installation. If there are errors, fix the install R script and rerun.  If a package was successfully downloaded and installed, it will not redo it again, it will see the package exists and will pick up where it left off.
+Review the generated output file, ''install-spatial-09052020.Rout'', for details on each package installation. If there are errors, fix the install R script and rerun.
 === Final List of R packages Installed ===
@@ Line 195: / Line 196: @@
 ==== VALET Package for R Packages ====
-Last step is to create a VALET package to load the correct version of R and your newly installed R packages.  The easiest way to do this is to copy the VALET package for the version of R you used for the installation, add your R_LIBS and load the dependent packages.  For this recipe, we will call the VALET package ''spatial-r.vpkg_yaml''
+Last step is to create a VALET package to load the correct version of R and your newly installed R packages.  The easiest way to do this is to copy the VALET package for the version of R you used for the installation, add your R_LIBS and load the dependent packages.  For this recipe, we will call the VALET package ''spatial-r.vpkg_yaml'' and it should be put in the workgroup ''sw'' directory in ''valet'' so it will be found when using your workgroup.
 <code bash>
-$ more spatial-r.vpkg_yaml
+[(it_css:traine)@login01 valet]$ pwd
+/work/it_css/sw/valet
+[(it_css:traine)@login01 valet]$ cat spatial-r.vpkg_yaml
 spatial-r:
   description:       The Comprehensive R Archive Network
@@ Line 229: / Line 232: @@
           value:        /work/it_css/sw/r/add-ons/r3.5.1/spatial-09052020/default
 </code>
+==== Testing R packages ====
+Now that you have installed your R packages, let's test by using VALET to setup our new environment by first clearing it and then using our new VALET package
+<code bash>
+[(it_css:traine)@login01 ~]$ vpkg_rollback all
+[(it_css:traine)@login01 ~]$ vpkg_require spatial-r
+</code>