GLIBCXX_3.4.26 not found in RCall

yakir12 · September 24, 2019, 2:11pm

If anyone has time to look at what must be a basic issue on my side, I’ve posted an issue on RCall.jl that is a show stopper for me:
https://github.com/JuliaInterop/RCall.jl/issues/339

Much if you can help out!

kdyrhage · September 24, 2019, 2:25pm

I just had the same problem when trying to import matplotlib with PyCall this morning. It worked fine in python, so I was a bit confused, but I came to the conclusion that the libstdc++ that ships with Julia is too old, while the one I have installed on my system is up to date. Compiling Julia from source fixed the problem.

yakir12 · September 24, 2019, 2:27pm

oooo, I’ll give it a shot!

kdyrhage · September 24, 2019, 2:32pm

Check that

$ strings /usr/lib64/libstdc++.so.6 | grep GLIBCXX

(or equivalent) returns GLIBCXX_3.4.26 before compiling, if not you need a newer version.

yakir12 · September 24, 2019, 2:54pm

Found it! Here:

$ /sbin/ldconfig -p | grep stdc++
        libstdc++.so.6 (libc6,x86-64) => /lib/x86_64-linux-gnu/libstdc++.so.6
$ strings /lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26 # <--- HERE IT IS!!!
GLIBCXX_3.4.27
GLIBCXX_3.4.28
GLIBCXX_DEBUG_MESSAGE_LENGTH

So what does that mean…?

yakir12 · September 24, 2019, 3:02pm

I’ll just add that this is still aproblem in the 1.3 rc2, incase that got updated between the two rcs…

yakir12 · September 24, 2019, 3:33pm

Just to sum it up, not sure what is going on, but I compiled Julia from source (v1.2.0) and it all works now.

Thanks for all the help!!!

laborg · January 3, 2020, 1:33pm

Tapped into this one today, but using a Julia source build isn’t a viable workaround. Setting LD_LIBRARY_PATH or R_LD_LIBRARY_PATH, as suggested in http://juliainterop.github.io/RCall.jl/stable/installation.html and some bug reports didn’t help either.

Has anyone gotten rid of this without compiling Julia?

R> library(devtools)
Loading required package: usethis
Error: package or namespace load failed for ‘usethis’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/gerhard/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/libs/Rcpp.so':
  /home/gerhard/julia-1.3.1/bin/../lib/julia/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /home/gerhard/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/libs/Rcpp.so)
Error: package ‘usethis’ could not be loaded

laborg · January 3, 2020, 2:35pm

I’ve seen your bug report:

https://github.com/JuliaInterop/RCall.jl/issues/339

Could you please reopen the issue?

laborg · January 4, 2020, 7:11am

Through help on Slack by @staticfloat it became clear that the underlying problem is, that the Julia provided libstdc++.so.6 is older than the one provided by the operating system, in my case Ubuntu 19.10, which in turn is used by R.

An intermediate solution is to replace Julias libstdc++.so.6 with the one from the OS:

# works for Ubuntu 19.10 64bit - match your locations accordingly!
 cp /usr/lib/x86_64-linux-gnu/libstdc++.so.6 $JULIA_HOME/lib/julia/

For completeness a list of references of this issue:

GLIBCXX_3.4.26 not found · Issue #339 · JuliaInterop/RCall.jl · GitHub (initial issue)
julia_setup (still) failing on Ubuntu 16.04 (Julia 1.1.1) · Issue #110 · Non-Contradiction/JuliaCall · GitHub (I think wrongly interpreted as just not finding the right so ) (I think wrongly interpreted as just not finding the right so )
Unable to load libjulia.so because `GLIBCXX_3.4.20' not found · Issue #1 · Non-Contradiction/JuliaCall · GitHub

yakir12 · January 7, 2020, 8:31am

Not sure where to discuss so doing so here. It seems like you, @laborg, have a good grasp on the issues here. Could you please add a note of sorts to both these repos, JuliaCall and RCall, informing users that run into the same problem on how to resolve these…? That would be a great first step until this gets permanently resolved (by having Julia use the system’s libstdc or updating Julia’s own libstdc in case the system’s version is higher or something).

laborg · January 7, 2020, 8:46am

Yes, good idea:
https://github.com/JuliaInterop/RCall.jl/pull/352

laborg · March 23, 2020, 6:02am

Backlink to the corresponding issue: libstdc++.so.6 is outdated and breaks RCall and others on recent Linux distros · Issue #34276 · JuliaLang/julia · GitHub

jfan · May 26, 2020, 3:25pm

This issue is not confined to RCall. PyCall also reports the same error. So, the problem is with the Julia distribution and the developers need to be alerted to this problem so that they have the most recent version of libstdc++.so.6 in the compiled version of Julia.

laborg · May 26, 2020, 6:44pm

The Julia developers are aware of the bug, see

github.com/JuliaLang/julia

libstdc++.so.6 is outdated and breaks RCall and others on recent Linux distros

opened 12:55PM - 06 Jan 20 UTC

closed 10:39PM - 08 Nov 22 UTC

laborg

As discussed on slack with and discourse ( https://discourse.julialang.org/t/gli…bcxx-3-4-26-not-found-in-rcall/29113/2 ) the problem of an outdated, bundled libstdc++ (e.g. Julia 1.3.1) compared to the libstdc++ provided by the OS (e.g. Ubuntu 19.10) is that it breaks RCall.jl when `Rcpp` is in play due to missing GLIBCXX symbols. I quote @staticfloat > So Ubuntu 19.10 is based on GCC 9, huh. We don't have a GCC 9 shard yet; we've been using GCC 7.2 on the buildbots (which correspondes to GLIBCXX_3.4.24), but there's no reason why we can't put our own libstdc++.so.6 into a julia binary-dist. Right now we've been bundling the libstdc++.so.6 that we get from the build environment, but it would be even better for us to just use an appropriate CompilerSupportLibraries_jll release, and craft those releases to be as compatible as possible (e.g. use the absolute newest libstdc++.so.6, the appropriate libgfortran.so.X, etc...) An intermediate workaround is described here: https://discourse.julialang.org/t/glibcxx-3-4-26-not-found-in-rcall/29113/11?u=laborg

I think its best is to attach your problem report there and hope that the proposed solution will soon come to fruition.

johnh · June 7, 2020, 10:35am

This is a stupid question.
If I build Julia from scratch on (say) a Fedora system or the latest Ubuntu where does the libstdc++ originate from?
IE. Does building from source build an up to date libstdc++ for that system.

Note to self - why dont you take the time to test that hypothesis…

giordano · June 7, 2020, 11:15am

If you build from scratch, I think the system libstdc++ is used and so it should work. The issues comes only from using the pre-built binary