libRmath-julia is not being installed in $JULIA_HOME./usr/lib

[dmbates]

This may be a problem with the makefiles in the julia/deps directory and not with Rmath per se. After the change to the name libRmath-julia the shared object does not seem to be installed in the julia/usr/lib directory when compiling a clean version of julia. If I run

make install-Rmath

in the deps directory the file becomes available.

Check the Travis reports for the Distributions package for the error.

[dmbates]

Perhaps the problem is more subtle. It seems that in julia/deps

make install-Rmath

installs the library in julia/usr/lib and then

make clean-Rmath

deletes it.

[ViralBShah]

Isn't that the correct behaviour for clean-Rmath? I will try a clean build.

[dmbates]

Perhaps I was wrong about make clean-Rmath being the culprit. In any case libRmath-julia.so is not in usr/lib after the build finishes on Ubuntu at least. As a result the Travis testing is failing for any package that uses a function in Distributions that relies on Rmath functions. See, e.g., StatsBase.jl

[ViralBShah]

Are you using USE_SYSTEM_RMATH by any chance? Perhaps that is what is happening on travis. The library is certainly getting installed in usr/lib.

Cc: @staticfloat

[ViralBShah]

There was a Makefile bug, I believe. Also, I am removing USE_SYSTEM_RMATH, as we use a patched Rmath.

[ViralBShah]

Please reopen if still not addressed.

[ViralBShah]

@staticfloat You may need to package libRmath-julia for travis.

[staticfloat]

@ViralBShah Removing USE_SYSTEM_RMATH means that I can't package libRmath-julia. :P

That flag was only ever there to install our own version of librmath that was packaged via the julia-deps repo. I will update the package on the repo now, however, as it's a long-overdue update.

[staticfloat]

@ViralBShah In julia-deps, there is now a librmath-julia package. We should transition Julia to using this in the docs and such so that we can close JuliaLang/julia#4341

[ViralBShah]

How about renaming USE_SYSTEM_RMATH to USE_SYSTEM_RMATH_JULIA or something so that people don't mistake it for the Rmath provided by R?

[staticfloat]

Sure, that could work.
-E

On Thu, Feb 13, 2014 at 6:00 PM, Viral B. Shah notifications@github.comwrote:

How about renaming USE_SYSTEM_RMATH to USE_SYSTEM_RMATH_JULIA or something
so that people don't mistake it for the Rmath provided by R?

Reply to this email directly or view it on GitHubhttps://github.com//issues/3#issuecomment-35048748
.

[sbos]

I'm not sure if this is a right place for my problem, but my installation of Julia (fresh built by homebrew on osx) misses libRmath-julia and I get expected errors like

ERROR: error compiling rand: error compiling rand!: could not load module libRmath-julia: dlopen(libRmath-julia.dylib, 1): image not found

[ViralBShah]

@staticfloat Perhaps we can avoid using system Rmath for homebrew builds?

[alyst]

I'm getting the same error as @sbos.
Please correct me, I believe it's because when Julia switched to not using system Rmath (see JuliaLang/julia@606b32ff), the conditional inclusion of Rmath-julia into JL_PRIVATE_LIBS was removed, but no unconditional inclusion was added. I've opened pull request JuliaLang/julia/pull/6093 to fix that. Is there a chance to merge it?

[staticfloat]

Hey there, sorry I've been incommunicado. I just did a fresh build of Homebrew julia and normal julia, and both worked fine, on a fresh OSX machine. How can I trigger this error?

[sbos]

Right now, homebrew build is broken for me. When julia starts I see the message

Warning: error initializing module LinAlg:
ErrorException("could not load module libopenblas: dlopen(libopenblas.dylib, 1): image not found")

But the error mentioned here is triggered by running

using Distributions
rand(Binomial(3, 0.5))
ERROR: error compiling rand: could not load module libRmath-julia: dlopen(libRmath-julia.dylib, 1): image not found

[staticfloat]

Can you type otool -L /usr/local/lib/libopenblas.dylib? I'm assuming your homebrew installation is in /usr/local/, but if it's not, feel free to modify that line to get the output we're looking for. That command should print out the libraries that libopenblas wants to load, and we can then track down the reason we're not loading them.

[sbos]

On my system, the only libopenblas found is the only one that had been installed by homebrew (is this a problem BTW?). It is located at /usr/local/Cellar/openblas64-julia/0.2.8/lib/libopenblas.dylib.

The output of otool is

/usr/local/Cellar/openblas64-julia/0.2.8/lib/libopenblas.dylib:
    /usr/local/opt/openblas64-julia/lib/libopenblas_sandybridgep-r0.2.8.dylib (compatibility version 0.0.0, current version 0.0.0)
    /usr/local/Cellar/gfortran/4.8.2/gfortran/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
    /usr/local/Cellar/gfortran/4.8.2/gfortran/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0)

[staticfloat]

@sbos I think I've managed to fix this problem. Please reinstall julia and try again.