Changes between Version 21 and Version 22 of cypress/R

Timestamp:

02/10/20 13:55:50 (4 years ago)

Author:

cbaribault

Comment:

Created link to separate page, "Installing R Packages on Cypress", and migrated content to that page accordingly.

cypress/R

@@ -326 +326 @@
 
 == [=#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)
-}}}
+See [wiki:InstallingRPackages  here.]
+