Changes between Version 2 and Version 3 of cypress/InstallingRPackages

Timestamp:

03/07/22 16:46:56 (2 years ago)

Author:

cbaribault

Comment:

Added section Capturing Logging Output From R Package Installation

cypress/InstallingRPackages

@@ -4 +4 @@
 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.
+
+For capturing logging output including error messages during installation, see [#CapturingRlogging below].
 
 For more information on how the R startup process works, see https://cran.r-project.org/web/packages/startup/vignettes/startup-intro.html
@@ -135 +137 @@
 }}}
 
+
+== [=#CapturingRlogging Capturing Logging Output From R Package Installation] ==
+
+When you install an R package, the logging output can include multiple screens of information before finally ending with a simple, brief indication of success or failure such as {{{installation of package 'RSQLite' had non-zero exit status}}}.
+
+As a result, any helpful diagnostic information can be easily lost - including one or more critical error messages that you may not notice as they scroll quickly and entirely out of view and out of your terminal window buffer.
+
+To avoid this loss of diagnostic information, the R function **install.packages()** provides an option **keep_outputs=T** (or **keep_outputs=TRUE**).
+
+You can use the **keep_outputs=T** option for capturing the logging output in files - one file per attempted R package - for your later inspection to look for possible error messages - as in the following.
+
+{{{
+> install.packages("RSQLite", keep_outputs=T)  # captures log output in a file RSQLite.out
+}}}
+
+Then from the BASH command line you can search for occurrences of the string {{{error:}}} either via **less** or **grep** BASH commands. (See [https://wiki.hpc.tulane.edu/trac/wiki/cypress/BasicLinuxComands#LinuxCommands Linux Commands].)
+
+For example in the following, multiple error messages captured in the file **RSQLite.out** indicate that the collection of boost C++ libraries is unexpectedly missing, which can be provided by loading the appropriate module, **boost/1.76.0**,  on Cypress. (See [https://wiki.hpc.tulane.edu/trac/wiki/cypress/ModuleCommand#Program:module Module Command].)
+
+{{{
+[tulaneid@cypress2 ~]$ grep -i error: RSQLite.out
+vendor/boost/preprocessor/list/fold_left.hpp(341): catastrophic error: cannot open source file "boost/preprocessor/list/detail/edg/fold_left.hpp"
+...
+vendor/boost/preprocessor/list/fold_left.hpp(341): catastrophic error: cannot open source file "boost/preprocessor/list/detail/edg/fold_left.hpp"
+ERROR: compilation failed for package ‘RSQLite’
+}}}
+
+The following excerpt is taken from the output in the R session of {{{> help("install.packages")}}}
+
+{{{
+keep_outputs: a logical: if true, keep the outputs from installing
+          source packages in the current working directory, with the
+          names of the output files the package names with ‘.out’
+          appended.  Alternatively, a character string giving the
+          directory in which to save the outputs.  Ignored when
+          installing from local files.
+}}}