How to specify (non-R) library path for dynamic library loading in R?
These libraries really should be standard on RH-based system too, and be found.
If you must add them to R, you have to do so before you start R. One way is via LD_LIBRARY_PATH, a better way is to edit a file in /etc/ld.so.conf.d/ (assuming RH/CentOS have that too). Else maybe via /etc/environment.
Edit: If /etc/ is out of reach, you can do everything below $HOME. Standard shell instantiation works, and R has its own .Rprofile and .Renviron. You can have those below $HOME for all your projects, and/or in a per-project directory---see help(Startup).
Are you running the code in RStudio Server? If so, the answer here may be useful.
I used to meet a similar error while loading dynamic library. The library was in a path contained in LD_LIBRARY_PATH. When I ran the code in R console, it could load the dynamic library correctly. But when I ran it in RStudio, the same error in your post raised.
The reason is that RStudio Server has its own library search path environment. You should specify the following configuration in /etc/rstudio/rserver.conf:
rsession-ld-library-path=/usr/lib64/:/usr/local/lib/:OTHER_PATH_OF_YOUR_LIB
Restart RStudio Server and the error should be fixed.
I put the export LD_LIBRARY_PATH=... statements into a file ~/.profile.
This way, both command line R and RStudio Server are able to find the shared library.
In my case, I was trying to get the Rglpk package to locate the libglpk.so file.
According to Stefaan Lippen's blog entry, the .profile file is the preferred location for these type of configurations not strictly related to bash.
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="+=")
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.