CODEWITHSUNDEEP
rxcodemacoscondadylib
O.rka
O.rka

Reputation: 30777

dyld: Library not loaded: @rpath/libreadline.6.2.dylib and @rpath/libintl.8.dylib

I just installed the new update on OSX because it kept popping up. Of course, it broke something. I can't access my R anymore.

Took me forever to get my environment set up. I have all of my R packages installed with the R I'm using in conda.

How can I fix this? Why do dyld libraries always break when I do any updates or slight tweaks? It really messes up the workflow...

Joshs-MBP:~ mu$ which R
/Users/mu/anaconda/bin/R
Joshs-MBP:~ mu$ R
dyld: Library not loaded: @rpath/libreadline.6.2.dylib
  Referenced from: /Users/mu/anaconda/lib/R/lib/libR.dylib
  Reason: image not found
Abort trap: 6
```

I'm running OSX Sierra 10.12.6 it literally broke immediately when it started updating Xcode (I thought it was just updating my iTunes). 

Joshs-MBP:~ mu$ conda info
Current conda install:

               platform : osx-64
          conda version : 4.3.29
       conda is private : False
      conda-env version : 4.3.29
    conda-build version : not installed
         python version : 3.6.3.final.0
       requests version : 2.18.4
       root environment : /Users/mu/anaconda  (writable)
    default environment : /Users/mu/anaconda
       envs directories : /Users/mu/anaconda/envs
                          /Users/mu/.conda/envs
          package cache : /Users/mu/anaconda/pkgs
                          /Users/mu/.conda/pkgs
           channel URLs : https://repo.continuum.io/pkgs/main/osx-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/osx-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/osx-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/osx-64
                          https://repo.continuum.io/pkgs/pro/noarch
            config file : None
             netrc file : None
           offline mode : False
             user-agent : conda/4.3.29 requests/2.18.4 CPython/3.6.3 Darwin/16.7.0 OSX/10.12.6
                UID:GID : 501:20

I tried https://github.com/ContinuumIO/anaconda-issues/issues/6312 but now there's a different but similar error:

Joshs-MBP:~ mu$ R
dyld: Library not loaded: @rpath/libintl.8.dylib
  Referenced from: /Users/mu/anaconda/lib/R/lib/libR.dylib
  Reason: image not found
Abort trap: 6

Upvotes: 6

Views: 10224

Answers (3)

herrlich10
herrlich10

Reputation: 6480

Had latest working Anaconda and R.

Tried conda update -c rdonnellyr -c main --all, but without luck.

Following https://github.com/conda/conda/issues/6183#issuecomment-830132824, duplicated and renamed anaconda3/lib/libreadline.8.1.dylib to anaconda3/lib/libreadline.6.2.dylib. The error message changed and started to complain about another lib, in my case, libicuuc.54.dylib, and then libicui18n.54.dylib. Repeated similar steps for them, and successfully got R to work in jupyter notebook.

However, rpy2 failed to run with the above work-around, because dlopen will check version-specific symbols inside the file and cannot be fooled simply by renaming the file.

This is probably a "mixing channel problem". Following https://conda-forge.org/docs/user/tipsandtricks.html, the issue was solved by installing r-essentials explicitly from conda-forge channel in a clean conda environment:

conda create --name r-tutorial pandas
conda activate r-tutorial
conda install -c conda-forge r-essentials
pip install rpy2

Upvotes: 2

Sunday Ikpe
Sunday Ikpe

Reputation: 984

Another option is to update r-base

$ conda update -n base r-base

This worked for me

Upvotes: 1

O.rka
O.rka

Reputation: 30777

https://github.com/conda/conda/issues/6183

Try : conda update -c rdonnellyr -c main --all

enter image description here

https://github.com/mingwandroid has a great explanation in what's happening with R, dylib, and MacOS

Upvotes: 2

Related Questions