[Rd] compiling C code using headers from another R package

Kevin Horan khoran at cs.ucr.edu
Tue Mar 12 17:30:35 CET 2013

     Thanks for your input. To clarify, I don't need to use any part of 
GSL in my R code, nor do I wish to make any part of it accessible to 
users of eiR. I need it to compile other C/C++ code (LSH KIT), which I 
did not write, that will itself be used in eiR.
     My goal is allow the user to install eiR without also having to 
install GSL before hand. The target audience is people in bioinformatics 
who may not how to install something like GSL. It seems like what I was 
suggesting is not such a good idea, if it will be hard to reliably find 
the header files from another R package. I could also push all of GSL 
into eiR, but as GSL has over 5000 files, this makes the package very 
large ( >22 MB) and  slow to compile. Both of which are a problem when 
submitting a package to bioconductor. It may very well be that leaving 
GSL as an external dependency to eiR is really the best and easiest way, 
but I just wanted to see if there was any way to make it easier for the 
user. So, any other suggestions about how this could be accomplished?  


On 03/12/2013 05:26 AM, Simon Urbanek wrote:
> Kevin,
> On Mar 11, 2013, at 5:20 PM, Kevin Horan wrote:
>> I am developing an R package, eiR,  which depends on another C library, GNU scientific library (GSL). In order to make life easier for the user, it would be nice to not have this as an external dependency, thus I would like to wrap this library in another R package, say GSLR for example. Thus far I know how to do this. The C code in eiR requires the .so library and the header files from GSL in order to compile. So the idea is that eiR would depend on GSLR, then GSLR gets compiled and installed first, then, while eiR is installing, it should be able to make use of the GSL library and header files while compiling. So my question is, how do I know where the GSL library and header files, packaged in GSLR, would live so I can point the compiler at them? I know how to find the installed directory of an R package from within R, but is there way to find that out using just Makevars or a Makefile? I'm open to suggestions about a better way organize all of this as well. I like the idea of keeping the GSL code separate so that it can be updated/changed independently from eiR though.
> Have a look at Rcpp.
>>     I'm also aware of the gsl R library on CRAN, however, this just wraps GSL in R functions, but I need to use the GSL C functions in other C code in eiR.
> Why is what you are proposing any better than simply using GSL in eiR? You will still need the GSL external dependency for GSLR and you are only adding a lot of complexity by linking into another package's external directory (you cannot use libs) which is in itself very tricky (you'll have to deal with both static and shared version, multi-arch setups, possible relocation etc.). It won't make it any easier on the user, rather to the contrary as there will be more things to break. The only reason Rcpp goes into such length to do this is because it has no choice (the Rcpp library has to use the same libR so cannot be used as external dependency) - I would certainly not recommend it for something as trivial as providing GSL.
> Cheers,
> Simon
>> Thanks.
>> Kevin
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