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--- technical:recipes:r-in-rlibs [2020-03-09 13:22] – anita
+++ technical:recipes:r-in-rlibs [2020-09-05 12:51] (current) – [VALET Package for R Packages] anita
@@ Line 1: / Line 1: @@
-===== Adding your own library of R modules in R_LIBS =====
+===== Adding your own library of R modules (packages) in R_LIBS =====
-These following instructions are adapted from [[software:r:caviness#personalprogram-specific-r-libraries-and-extensions|installing personal/program specific R libraries and extensions]] on Caviness.
+The following instructions were adapted from [[software:r:caviness#personalprogram-specific-r-libraries-and-extensions|installing personal/program specific R libraries and extensions]] on Caviness.
 ==== List of packages requested to be installed ====
-  * \*rlang - needed to install an updated version for other requested packages
+  * **rlang** - needed to install an updated version for other requested packages
-  * \*Rcpp - needed to install an updated version for other requested packages
+  * **Rcpp** - needed to install an updated version for other requested packages
   * ranger  - install first gets loaded by VSURF
   * randomForest
@@ Line 17: / Line 17: @@
   * rasterVis
   * Raster
-  * \*units - needed to install an updated version for other requested packages
+  * **units** - needed to install an updated version for other requested packages
-  * \*sf - needed updated version
+  * **sf** - needed updated version
-  * \*reproducible - needed updated version
+  * **reproducible** - needed updated version
   * SpaDES
   * foreach
@@ Line 27: / Line 27: @@
   * ggplot2
-\* not requested, but necessary in order to update the R packages requested.
+Packages in **bold** were not requested, but necessary in order to update the R packages requested.
-There is much research required to determine what other software needs to be loaded via VALET, plus which packages need to be updated and in what order so the list of requested packages will install correctly. For this example, SpaDES, is the library of R modules we want to install so you should use [[https://cran.r-project.org/web/packages/SpaDES/index.html|SpaDES: Develop and Run Spatially Explicit Discrete Event Simulation Models]] to see the dependencies and imports required.  This step should be repeated for each package.
+There is much research required to determine what other software needs to be loaded via VALET, plus which packages need to be updated and in what order so the list of requested packages will install correctly. For example, SpaDES, is one of the packages we want to install so use [[https://cran.r-project.org/web/packages/SpaDES/index.html|SpaDES: Develop and Run Spatially Explicit Discrete Event Simulation Models]] to see the dependencies and imports required.  This step should be repeated for each package.
+==== Preparations ====
+Make sure you [[abstract:caviness:system_access:|connect to Caviness]] with X11 enable (Xming for Windows, XQuartz for Mac) before starting as some of the packages need X11 to compile properly.
+Next make sure you are in your [[abstract:caviness:app_dev:compute_env#using-workgroup-and-directories|workgroup]] (ie. ''workgroup -g <<//investing_entity//>>''). We will be using account ''traine'' in workgroup ''it_css'' for this recipe.
+<code bash>
+[traine@login01 ~]$ workgroup
+[(it_css:traine@login01 ~]$
+</code>
+Next choose a directory in which to install the R packages.  This will depend on a number of factors, but mostly the version of R. The strings ''«r-version»'' and ''«rpkgs-date»'' will denote the version of R and the name chosen for the R packages dated -- this recipe will use ''r3.5.1'' and ''spatial-09052020''.  Do not locate this directory under the ''/lustre/scratch'' file system; typically a directory under the workgroup's storage is appropriate:
+  * If adding the R libraries for multiple users in the workgroup, choose ''${WORKDIR}/sw/r/add-ons/«r-version»/«rpkgs-date»/default'' as the base directory.
+  * If the R libraries are solely for personal use, choose ''${WORKDIR}/users/<username>/sw/r/add-ons/«r-version»/«rpkgs-date»/default'', for example.
+Note that these examples assume a standard [[abstract:caviness:install_software:|workgroup storage]] layout with group-writable ''sw'' and ''users'' directories at the top level.  Create the directory:
+<code bash>
+[(it_css:traine)@login01 ~]$ mkdir -p ${WORKDIR}/sw/r/add-ons/r3.5.1/spatial-09052020/default
+</code>
+Now load all the packages via VALET that are needed to install the R libraries and add the new path to the ''R_LIBS'' environment variable for the installation.  Due to the number of packages and environment variables required, it is best to create a script called ''setup-«rpkgs-date».sh''using ''nano'' or ''vim''.  The script for this recipe will be called ''[(it_css:traine)@login01 ~]$'' aserves as a document for future installations to know what packages and environment variables were required for the installation.
+<code bash>
+[(it_css:traine)@login01 ~]$ cat setup-spatial-09052020.sh
+#!/bin/bash
+# usage: source install-spatial-09052020.sh
+# clear environment
+vpkg_rollback all
+# Load software via VALET and set environment variables
+# that are needed to install requested R packages:
+# ranger VSURF plyr randomForest ipred e1071 quantregForest
+# car rgdal raster rasterVis SpaDES foreach doParallel
+# openxlsx DescTools ggplot2
+vpkg_devrequire r/3.5.1:mkl-thr
+vpkg_devrequire r-cran/3.5.1:20180715
+vpkg_devrequire gdal/2.3.0
+vpkg_devrequire proj/5.1.0
+vpkg_devrequire netcdf/4.6.1
+vpkg_devrequire udunits/2.2.26
+export UDUNITS2_LIBS=${UDUNITS_PREFIX}/lib
+export UDUNITS2_INCLUDE=${UDUNITS_PREFIX}/include
+vpkg_devrequire geos/3.6.2
+export GEOS_DIR=${GEOS_PREFIX}
+# Add the new R library path created to the R_LIBS environment for R to find
+# (i.e.) based creating the directory using
+# "mkdir -p ${WORKDIR}/sw/r/add-ons/r3.5.1/spatial-09052020/default" (see above)
+R_LIBS="${WORKDIR}/sw/r/add-ons/r3.5.1/spatial-09052020/default:${R_LIBS}"
+# display R_LIBS with the new R libraries directory added
+echo ${R_LIBS}
+</code>
+Now that we have the setup script, we can run it to setup our environment needed before installing the R packages by doing
+<code bash>
+[traine@login01 ~]$ source install-spatial-09052020.sh
+ERROR:  no previous session on record, unable to roll back
+Adding dependency `gcc/4.9.4` to your environment
+Adding dependency `intel/2018u4` to your environment
+Adding package `r/3.5.1:mkl-thr` to your environment
+Adding package `r-cran/3.5.1:20180715` to your environment
+Adding package `gdal/2.3.0` to your environment
+Adding package `proj/5.1.0` 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 package `netcdf/4.6.1` to your environment
+Adding package `udunits/2.2.26` to your environment
+Adding package `geos/3.6.2` to your environment
+/opt/shared/r/add-ons/r3.5.1/cran/20180715
+/work/it_css/sw/r/add-ons/r3.5.1/spatial-09052020/default:/opt/shared/r/add-ons/r3.5.1/cran/20180715
+[(it_css:traine)@login01 ~]$
+</code>
+The first time you run the above script it will give you a VALET ''ERROR:  no previous session on record, unable to roll back'' if you have not loaded any other packages with VALET prior to running it.
+==== Install the R Packages ====
+In most cases, creating a R script using ''nano'' or ''vim'' will be necessary due to the large number of packages and information required to install each package such as ''install-«rpkgs-date».R''. Using a R script is better suited due to the amount of typing, potential mistakes, changes required based on errors, and again a way of documenting your steps for future installations. For this example we will call it ''install-spatial-09052020.R'' to match our setup script naming convention.
+<code bash>
+[(it_css:traine)@login01 ~]$ cat install-spatial-09052020.R
+# usage: R CMD BATCH install-spatial-09052020.R &
+.libPaths()
+chooseCRANmirror(ind = 56)
+install.packages("rlang", type = "source", dependencies=TRUE)
+library(rlang)
+install.packages("Rcpp", type = "source", dependencies=TRUE)
+library(Rcpp)
+install.packages("ranger", 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(ranger)
+install.packages("randomForest", 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(randomForest)
+install.packages("VSURF", 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(VSURF)
+install.packages("plyr", 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(plyr)
+install.packages("ipred", 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(ipred)
+install.packages("e1071", 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(e1071)
+install.packages("quantregForest", 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(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("sf", dependencies = TRUE)
+library(sf)
+install.packages("reproducible", type = "source", dependencies = TRUE)
+library(reproducible)
+install.packages("SpaDES", 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(SpaDES)
+library(foreach)
+library(doParallel)
+library(openxlsx)
+library(DescTools)
+library(ggplot2)
+</code>
+Now install the R libraries by running the R script as follows
+<code bash>
+[traine@login01 ~]$ R CMD BATCH install-spatial-09052020.R &
+[traine@login01 ~]$
+</code>
+and by using ''&'' it will run the R script in the background since this installation may take a long time depending on the number of packages. An output file called ''install-spatial-rpkgs.Rout'' is created to keep track of the installation.  You can watch the progress by using
+<code>
+[traine@login01 ~]$ tail install-spatial-09052020.Rout
+</code>
+=== 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.
+=== Final List of R packages Installed ===
+<code bash>
+$ ls $WORKDIR/sw/r/add-ons/r3.5.1/spatial-09052020/default
+car        leafem    quantregForest  rgdal          SpaDES.tools
+dplyr      leaflet   quickPlot       rgeos          stars
+e1071      leafpop   randomForest    rlang          tibble
+ellipsis   leafsync  ranger          scales         tidyselect
+fansi      mapview   raster          sf             units
+gdalUtils  ncdf4     rasterVis       SpaDES         vctrs
+ggforce    pillar    Rcpp            SpaDES.addins  VSURF
+ipred      plyr      reproducible    SpaDES.core
+</code>
+==== VALET Package for R Packages ====
+Last step is to create a VALET package to load the correct version of R and your newly installed R packages.  The easiest way to do this is to copy the VALET package for the version of R you used for the installation, add your R_LIBS and load the dependent packages.  For this recipe, we will call the VALET package ''spatial-r.vpkg_yaml'' and it should be put in the workgroup ''sw'' directory in ''valet'' so it will be found when using your workgroup.
+<code bash>
+[(it_css:traine)@login01 valet]$ pwd
+/work/it_css/sw/valet
+[(it_css:traine)@login01 valet]$ cat spatial-r.vpkg_yaml
+spatial-r:
+  description:       The Comprehensive R Archive Network
+  url:               http://cran.us.r-project.org/
+  prefix:            /opt/shared/r/add-ons
+  default-version:   "3.5.1:20180715"
+  development-env:   false
+  actions:
+    - action:        path-prepend
+      variable:      R_LIBS
+      value:         ${VALET_PATH_PREFIX}
+  versions:
+    "3.5.1:20180715":
+      description:   CRAN snapshot from 07/15/2018, includes 11,486 R modules
+      prefix:        r3.5.1/cran/20180715
+      dependencies:
+        -            r/3.5.1:mkl-thr
+        -            gdal/2.3.0
+        -            proj/5.1.0
+        -            netcdf/4.6.1
+        -            udunits/2.2.26
+        -            geos/3.6.2
+      actions:
+        - action:       path-prepend
+          variable:     R_LIBS
+          value:        /work/it_css/sw/r/add-ons/r3.5.1/spatial-09052020/default
+</code>
+==== Testing R packages ====
+Now that you have installed your R packages, let's test by using VALET to setup our new environment by first clearing it and then using our new VALET package
+<code bash>
+[(it_css:traine)@login01 ~]$ vpkg_rollback all
+[(it_css:traine)@login01 ~]$ vpkg_require spatial-r
+</code>