Rename libRmath to libRmath-julia

[ViralBShah]

I would like to remove the Rmath build to be removed from julia. Eventually, Rmath dependency can be completely removed as discussed in this PR, but until then, it can be made available through RmathDist.jl.

JuliaStats/Distributions.jl#138

[ViralBShah: Originally this discussion started with removing Rmath, but we decided to just change the filename and remove Rmath in 0.4]

[ViralBShah]

Cc: @johnmyleswhite @dmbates

This should make it easier to ship julia in linux distros by avoiding the conflict with R's libRmath.

Cc: @nalimilan @sebastien-villemot

[staticfloat]

+1

I'm impressed that I had the reflexes to reference this issue immediately. Good work, me. ;)

[JeffBezanson]

+1

It would be great to remove this ASAP.

[johnmyleswhite]

I'm cool with this if @simonbyrne is willing to have Distributions depend on RMathDist until we finish our work to remove all dependency on Rmath.

[simonbyrne]

@johnmyleswhite As it stands, RmathDist.jl actually depends on Distriibutions.jl (as it borrows its interface). My thought was that perhaps users who need the functionality that has yet to be finished (such as noncentral distributions) could use that until we're up to speed. I think doing it the other way around (i.e. making Distributions.jl depend on RmathDist.jl) would be a lot of extra hassle, especially since its only meant to be a temporary measure.

[stevengj]

Would be nice to have a checklist of functions from libRmath that need to be replaced... I don't see any usages in Base?

[simonbyrne]

@stevengj As far as I know, it isn't used Base at all, and the only package to use it is Distributions.jl.

[ViralBShah]

I propose that we rename libRmath.jl to libRmath-julia.jl since it is a customized build. What all packages would be affected with this renaming change?

@johnmyleswhite Will this lead to an extra barrier in terms of adoption of Julia for stats? Building something through BinDeps is something that only a small percentage of our users will be able to do successfully. Thinking about this a bit more, I think that renaming the file will fix the conflict with R on various distros, but we should only remove it from Base once Distributions stops using it completely.

[johnmyleswhite]

Shipping a renamed libRmath seems like a great solution to me. I think we can probably get rid of Rmath by the 0.4 release.

[ViralBShah]

@johnmyleswhite If I just rename it - could you update any packages that depend on it?

[ViralBShah]

Fixed in 94ebea0

[ViralBShah]

@sebastien-villemot @staticfloat @nalimilan The renaming of libRmath to libRmath-julia should remove any conflicts that the julia installation has with any other system provided files.

[ViralBShah]

@johnmyleswhite I have updated Distributions. Perhaps we need to do a version bump? Would be great if you can try it out and bump.

[johnmyleswhite]

Thanks, Viral!

This seems to work except for some weird warnings about nnz. I want to figure out what's causing them before releasing this.

[rickhg12hs]

$ grep -C 3 nnz base/deprecated.jl 

# 0.3 discontinued functions

function nnz(X)
    depwarn("nnz has been renamed to countnz and is no longer computed in constant time for sparse matrices. Instead, use nfilled() for the number of elements in a sparse matrix.", :nnz)
    countnz(X)
end
export nnz

[nalimilan]

@ViralBShah Actually I don't really care about the name of the library since it's installed in a private dir. (Of course it's cleaner to change the name since the code is slightly different from upstream.)

[staticfloat]

I think the big compatibility problem is the header names. And those are
due to my Ubuntu package. I should probably just delete them since we don't
use the headers at all.
On Feb 8, 2014 10:49 AM, "Milan Bouchet-Valat" notifications@github.com
wrote:

@ViralBShah https://github.com/ViralBShah Actually I don't really care
about the name of the library since it's installed in a private dir. (Of
course it's cleaner to change the name since the code is slightly different
from upstream.)

Reply to this email directly or view it on GitHubhttps://github.com//issues/5524#issuecomment-34552182
.

[lindahua]

@johnmyleswhite I have taken care of the nnz warnings. It is due to a recent renaming from nnz to countnz in the Base.

[johnmyleswhite]

Should I bump the Distributions version number?

[ViralBShah]

@nalimilan Good to know that it is in a private place, but I think this makes things clearer.
@johnmyleswhite I think it is safe to bump the version number.