How to Specify (Non-R) Library Path for Dynamic Library Loading in R

How to specify (non-R) library path for dynamic library loading in R?

Normally, the iconv method is picked up from glibc, which is linked to during build of the R packages in question. For whatever reason, however, iconv is getting resolved to libiconv in this case, but it is not linked by the R packages during build.

Original Workaround

One can make the linking to libiconv explicit by adding the following line to the haven/src/Makevars source file

PKG_LIBS=-liconv

which then let's you install from source R CMD INSTALL haven. However, editing packages feels hacky, plus this is something that will need to be done every upgrade, which sounds like a hassle.

Cleaner Workaround

Another option is to use withr::with_makevars, which allows one to temporarily control Makevars content. With this technique, one can install directly from the repo:

withr::with_makevars(c(PKG_LIBS="-liconv"), install.packages("haven"), assignment="+=")

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Credit: @knb suggested that I inspect the readxl.so with ldd and this turned out to be super useful because it showed that the shared object wasn't even trying to link to libiconv. Knowing that, I realized I could manually add the reference via the -liconv flag. Thanks @knb!

Additional Info

On the package side of things, relevant details about connecting libraries to R packages can be found in the guide for building libraries. On the system configuration side, the R-admin guide has some useful sections.

How do I change the default library path for R packages

See help(Startup) and help(.libPaths) as you have several possibilities where this may have gotten set. Among them are

• setting R_LIBS_USER
• assigning .libPaths() in .Rprofile or Rprofile.site

and more.

In this particular case you need to go backwards and unset whereever \\\\The library/path/I/don't/want is set.

To otherwise ignore it you need to override it use explicitly i.e. via

library("somePackage", lib.loc=.libPaths()[-1])

when loading a package.

Change R default library path using .libPaths in Rprofile.site fails to work

I generally try to keep all of my packages in one library, but if you want to add a library why not append the new library (which must already exist in your filesystem) to the existing library path?

.libPaths( c( .libPaths(), "~/userLibrary") )
 # obviously this would need to be a valid file directory in your OS
 # min just happened to be on a Mac that day

Or (and this will make the userLibrary the first place to put new packages):

.libPaths( c( "~/userLibrary" , .libPaths() ) )

Then I get (at least back when I wrote this originally):

> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/2.15/Resources/library"
[2] "/Users/user_name/userLibrary"  

The .libPaths function is a bit different than most other nongraphics functions. It works via side-effect. The functions Sys.getenv and Sys.setenv that report and alter the R environment variables have been split apart but .libPaths can either report or alter its target.

The information about the R startup process can be read at ?Startup help page and there is RStudio material at: https://support.rstudio.com/hc/en-us/articles/200549016-Customizing-RStudio

In your case it appears that RStudio is not respecting the Rprofile.site settings or perhaps is overriding them by reading an .Rprofile setting from one of the RStudio defaults. It should also be mentioned that the result from this operation also appends the contents of calls to .Library and .Library.site, which is further reason why an RStudio- (or any other IDE or network installed-) hosted R might exhibit different behavior.

Since Sys.getenv() returns the current system environment for the R process, you can see the library and other paths with:

Sys.getenv()[ grep("LIB|PATH", names(Sys.getenv())) ]

The two that matter for storing and accessing packages are (now different on a Linux box):

R_LIBS_SITE                          /usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
R_LIBS_USER                          /home/david/R/x86_64-pc-linux-gnu-library/3.5.1/
 

how to set lib-paths in R to have a single directory which is C:\Users\Username\Documents\...

Hong Ooi's answer: "You can't, and you don't want to, remove the base library location. That's where R's own packages live, and without them you can't use R."

Setting a directory path to a dynamically linked library in an R package

The standard way to do this, as described in Writing R Extensions, is:

1.5.4 useDynLib

A NAMESPACE file can contain one or more useDynLib directives which allows shared objects that need to be loaded.* The directive

useDynLib(foo)

registers the shared object foo** for loading with library.dynam. Loading of registered object(s) occurs after the package code has been loaded and before running the load hook function. Packages that would only need a load hook function to load a shared object can use the useDynLib directive instead.

* NB: this will only be read in all versions of R if the package contains R code in a R directory.
** Note that this is the basename of the shared object, and the appropriate extension (.so or .dll) will be added.

Setting LD_LIBRARY_PATH from inside R

With help from Hans Lub, the way to solve the problem is by using the dyn.load() function and supplying the full path to the library:

dyn.load('path_to_library')

and then, loading via library should work.

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