Changes between Version 10 and Version 11 of cypress/R

Timestamp:

08/21/17 16:50:36 (7 years ago)

Author:

cbaribault

Comment:

CEB 20170821 - Added multiple alternatives for installing R packages.

cypress/R

@@ -201 +201 @@
 
 
-== Installing Packages into user home directory ==
-If you want to use some packages but those aren't installed into the R on Cypress,
-you can install those into your home directory.
-
-First, create a directory and set an environmental variable,
-{{{
-mkdir -p ~/R/Library
-export R_LIB_USER=/home/USERID/R/Library
+== Installing R Packages into user home directory or lustre sub-directory ==
+If you want to use some R packages that are not yet installed in your desired version of R on Cypress,
+then you have several alternatives - depending on your desired level of reproducibility.
+
+=== Alternative 1 - default to home sub-directory ===
+From your R session, you may choose to have R install its packages into a sub-directory under your home directory.
+By default R will create such a sub-directory whose name corresponds to the R version of your current R session and install your packages there.
+
+{{{
+> R.version.string
+[1] "R version 3.4.1 (2017-06-30)"
+> install.packages("copula")
+Installing package into ‘/share/apps/spark/spark-2.0.0-bin-hadoop2.6/R/lib’
+(as ‘lib’ is unspecified)
+Warning in install.packages("copula") :
+  'lib = "/share/apps/spark/spark-2.0.0-bin-hadoop2.6/R/lib"' is not writable
+Would you like to use a personal library instead?  (y/n) y
+Would you like to create a personal library
+~/R/x86_64-pc-linux-gnu-library/3.4
+to install packages into?  (y/n) y
+...
+}}}
+
+=== Alternative 2 - specify your lustre sub-directory via exported environment variable ===
+Alternatively, if you prefer to use, say, your lustre sub-directory rather than your home directory, then you may do so via an exported environment variable setting as in the following.
+The environmental variable **R_LIBS_USER** points the desired location of user package(s).
+
+First, create a directory and export the environment variable.
+{{{
+mkdir -p /lustre/project/<your-group-name>/R/Library
+export R_LIB_USER=/lustre/project/<your-group-name>/R/Library
 }}} 
-The environmental variable R_LIBS_USER points the location of user package.
-Setting in ~/.Renviron to tell R a default location,
-{{{
-echo 'R_LIBS_USER="~/R/Library"' > $HOME/.Renviron
+
+Then run R and install a package. Note that we can use the R function **.libPaths()** as confirmation of the user library location.
+{{{
+> .libPaths()
+[1] "/lustre/project/<your-group-name>/R/Library"
+[2] "/share/apps/spark/spark-2.0.0-bin-hadoop2.6/R/lib"
+[3] "/share/apps/R/3.4.1-intel/lib64/R/library"
+> install.packages("copula")
+Installing package into ‘/lustre/project/<your-group-name>/R/Library’
+(as ‘lib’ is unspecified)
+...
+}}}
+
+=== Alternative 3 - specify lustre sub-directory via environment file ===
+Similarly, you may accomplish the above via the same environment variable setting as above but in a local file as in the following.
+
+First, create a directory as above.
+{{{
+mkdir -p /lustre/project/<your-group-name>/R/Library
+}}}
+Then setting **R_LIBS_USER** in the file **~/.Renviron** will tell R a default location.
+
+Note however that setting or unsetting the environment variable **R_LIBS_USER** in the file **~/.Renviron** will //override// any previously exported value of that same environment variable!
+
+{{{
+echo 'R_LIBS_USER="/lustre/project/<your-group-name>/R/Library"' > ~/.Renviron
+}}}
+Or use a text editor in order to create and edit the file **~/.Renviron** so that the file includes the following line.
+{{{
+R_LIBS_USER="/lustre/project/<your-group-name>/R/Library"
+}}}
+
+Then run R and install a package. Note again the use of R function **.libPaths()** as confirmation of the user library location.
+{{{
+> .libPaths()
+[1] "/lustre/project/<your-group-name>/R/Library"
+[2] "/share/apps/spark/spark-2.0.0-bin-hadoop2.6/R/lib"
+[3] "/share/apps/R/3.4.1-intel/lib64/R/library"
+> install.packages("copula")
+Installing package into ‘/lustre/project/<your-group-name>/R/Library’
+(as ‘lib’ is unspecified)
+...
+}}}
+
+=== Alternative 4 - specify lustre sub-directory via R profile file ===
+Similarly, you may set the sub-directory depending on R major.minor version via the R profile file as in the following.
+
+Edit the file **~/.Rprofile** as follows.
+{{{
+majorMinorPatch <- paste(R.version[c("major", "minor")], collapse=".")
+majorMinor <- gsub("(.*)\\..*", "\\1", majorMinorPatch)
+#print(paste0("majorMinor=", majorMinor))
+myLibPath <- paste0("/lustre/project/<your-group-name>/R/Library/", majorMinor)
+dir.create(myLibPath, showWarnings = FALSE)
+#print(paste0("myLibPath=", myLibPath))
+newLibPaths <- c(myLibPath, .libPaths())
+.libPaths(newLibPaths)
+}}}
+
+Note however that setting the R library trees directly via **.libPaths()** in the file **~/.Rprofile** will //override// any previously set value of **R_LIBS_USER**!
+
+Then run R and install a package. Note again the use of R function **.libPaths()** as confirmation of the user library location.
+{{{
+> .libPaths()
+[1] "/lustre/project/<your-group-name>/R/Library/3.4"
+[2] "/share/apps/spark/spark-2.0.0-bin-hadoop2.6/R/lib"
+[3] "/share/apps/R/3.4.1-intel/lib64/R/library"
+> install.packages("copula")
+Installing package into ‘/lustre/project/<your-group-name>/R/Library/3.4’
+(as ‘lib’ is unspecified)
+...
+}}}
+
+=== Alternative 5 - specify lustre sub-directory via R code ===
+As for yet another alternative, you can accomplish the above entirely in your R code via the following.
+First, create a directory as before.
+{{{
+mkdir -p /lustre/project/<your-group-name>/R/Library
 }}} 
-Or use a text editor.
-
-Run R and install a package
-{{{
-> install.packages("copula",lib="~/R/Library")
+
+Then run R and install a package, but note that you must also specify the location from which to load the package in the ensuing call to the R function **library()**.
+{{{
+> myLib := "/lustre/project/<your-group-name>/R/Library"
+> install.packages("copula",lib=myLib)
+...
+> library(copula, lib.loc=myLib)
 }}}