Changes between Initial Version and Version 1 of cypress/InstallingRPackages

Timestamp:

02/10/20 13:38:36 (6 years ago)

Author:

cbaribault

Comment:

Created separate wiki page for installing R packages on Cypress.

cypress/InstallingRPackages

@@ +1 @@
+[[PageOutline]]
+
+== [=#InstallingRPackages Installing R Packages on Cypress] ==
+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, as prescribed below, for locations for installing those packages. Those locations include either your user home directory or lustre sub-directory, and the methods will vary depending on your desired level of reproducibility.
+
+=== [=#RPackageAlternative1 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
+--- Please select a CRAN mirror for use in this session ---
+PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
+HTTPS CRAN mirror
+
+ 1: 0-Cloud [https]                   2: Algeria [https]
+...
+79: Vietnam [https]                  80: (HTTP mirrors)
+
+
+Selection: 77
+...
+}}}
+
+Note that the above example was performed without X11 forwarding, resulting in a prompt at the command line for selection of a CRAN mirror site in the above, at which point you should enter the number corresponding to the desired mirror site, e.g. '''77'''.
+
+=== 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_LIBS_USER=/lustre/project/<your-group-name>/R/Library
+}}} 
+
+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 that setting the R library trees directly via the R function **.libPaths()** in the file **~/.Rprofile** can thus either //override// or //append// to that of 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
+}}} 
+
+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)
+}}}
+