Problems reloading C++ code with devtools::load_all when using RcppArmadillo

[Mike P]

Hi,

It seems that devtools::load_all does not reload shared library after re-compiling new changes in C++ code. I have to restart R for my changes to take effect. This only happens when I use armadillo library. Below example is reproducible every time.

To reproduce, start a new R session and do:

> library(devtools)

> library(RcppArmadillo)

> RcppArmadillo.package.skeleton("armatest")

Then edit the generated armatest/src/rcpparma_hello_world.cpp file and add the following function at the end:

// [[Rcpp::export]]

Rcpp::NumericVector see_change() {

  Rcpp::NumericVector v(1);

  v[0] = 1;

  return v;

}

Then compile and load the package, and call the function in the R session:

> load_all("armatest")

> see_change()

[1] 1

Now make a small change to the above C++ function by changing "v[0]=1" to "v[0]=2". In the same R session reload the package and run the function again:

> load_all("armatest")

> see_change()

[1] 1

Notice that the output hasn't changed, even though the C++ code was compiled and the shared library was supposedly reloaded. However if I restart R and load the package again, the output does change to 2. Also notice that doing load_all on this package in the new R session doesn't recompile anything, which means that compilation was done properly in the previous R session, and the problem is only that the new shared library was not reloaded.

I'm running Ubuntu 14.04. Here are some details about my system:

> R.version

               _                           

platform       x86_64-pc-linux-gnu         

arch           x86_64                      

os             linux-gnu                   

system         x86_64, linux-gnu           

status                                     

major          3                           

minor          2.2                         

year           2015                        

month          08                          

day            14                          

svn rev        69053                       

language       R                           

version.string R version 3.2.2 (2015-08-14)

nickname       Fire Safety                 

> packageVersion("devtools")

[1] ‘1.9.1’

> packageVersion("Rcpp")

[1] ‘0.12.1’

> packageVersion("RcppArmadillo")

[1] ‘0.5.500.2.0’

The armadillo library has version 4.200.0 and is from the official Ubuntu installation.

Thanks for any help on this.

-Mike

[Mike P]

I've a solution and going to post it here for reference for other people.

I've begun experimenting with the produced shared library armatest.so by loading/unloading it using R function dyn.load/dyn.unload. The functions seemed to work correctly, but when using lsof on my R process, I've noticed that the library remained loaded. So dyn.unload was not actually unloading the library, and it remained mapped in the process memory.

Following suggestions in this thread:

https://github.com/kaskr/adcomp/issues/27

I've ran readelf on the shared library, and sure enough it contained symbols labeled UNIQUE:

$ readelf -s armatest.so | grep UNIQUE
   118: 000000000020d248     8 OBJECT  UNIQUE DEFAULT   24 _ZZN4arma16arma_stream_er
   127: 000000000020d7c8     8 OBJECT  UNIQUE DEFAULT   25 _ZN4arma5DatumIdE3nanE
   133: 000000000020d240     8 OBJECT  UNIQUE DEFAULT   24 _ZZN4arma16arma_stream_er
   182: 000000000020d7c0     8 OBJECT  UNIQUE DEFAULT   25 _ZGVN4arma5DatumIdE3nanE
   179: 000000000020d240     8 OBJECT  UNIQUE DEFAULT   24 _ZZN4arma16arma_stream_er
   211: 000000000020d7c0     8 OBJECT  UNIQUE DEFAULT   25 _ZGVN4arma5DatumIdE3nanE
   214: 000000000020d248     8 OBJECT  UNIQUE DEFAULT   24 _ZZN4arma16arma_stream_er
   262: 000000000020d7c8     8 OBJECT  UNIQUE DEFAULT   25 _ZN4arma5DatumIdE3nanE

Again from the above thread, I've added this to my Makevars, and the problem disappeared!:

PKG_CXXFLAGS=-fno-gnu-unique

With this flag I'm now able to reload the library using devtools::load_all and all my changes take effect immediately. No more restarting R after changing C++ code.

-Mike