Monthly Archives: December 2015

R CMD INSTALL with symlink to R

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Problems with R CMD INSTALL

I was trying to install a package (ANTsR) by running R CMD INSTALL as normal on the cloned github repository on a particular cluster. I kept getting errors and could not understand why for the life of me. Note, I have not used this cluster much and wasn't sure how it was configured.

I was pretty sure that this was a configuration problem on the cluster because I had installed this repo on:

  1. My system
  2. A shiny server
  3. Another cluster

Finding the Error

The build was using cmake, so I figured it was some flag. Oddly enough, I was getting the error (I put . where thes are hard paths not relevant to you):

-- Check for working C compiler: ./cc -- broken
CMake Error at . (message):
  The C compiler "." is not able to compile a simple test program.

Whoa. Now either the C compiler is broken (unlikely) or the configuration has an error/bug (much more likely). I didn't write the config for this package (it's pretty complex), so I felt a bit at a loss.

Let's look at the error

Well, the error did push me to the log for the error CMakeFiles/CMakeError.log, let's go there. Looking at the result of CMakeFiles/CMakeError.log, I found the following areas that seemed like where things were problems:

Build flags: ;WARNING:;ignoring;environment;value;of;R_HOME

Hmm. I see that these are words, not really building flags. They also seem like R code. I don't know how they got there, so I did some Googling.

I got to a page of someone having a similar issue: '“ignoring environment value of R_HOME” error when installing packages'. That sounds like my problem. OK their admin reset R_HOME and everything is great. Good for him, not much help for me.

I found a bug report for R which discusses this, but there didn't seem to be any resolution.

Finding a Solution

I went back to the simple R warning “WARNING: ignoring environment value of R_HOME” and found an old StackOverflow Post about it.

Now, one thing they discussed was 

unset R_HOME

I tried that, nothing worked.

OK, well what about RHOME, let's unset that too:

unset RHOME

Error, fail. Moreover, these variables were never set anyway. Oh! I realized if we reversed the error, that R_HOME was set incorrectly, then let's just set it before R CMD INSTALL and then it shouldn't error:

R_HOME=`R RHOME`;
R CMD INSTALL ANTsR

That's not to say the package will install without a hitch, but this part of the build seems to be fixed. (Note: I had to clean out the errors to rerun).

Why did this happen?

I believe most of this happened by the configuration of R on the cluster and the linking of the R folder (try which R) to the true home for R (try R RHOME). I don't know where (if anywhere) in the setup/.bashrc/.bash_profile scripts R_HOME is set, but it seems that this discrepancy caused a problem.