Jupyter R kernel crashes

(TEMP FIX ONLY)

See this discussion: https://groups.google.com/a/continuum.io/forum/#!topic/conda/nqPfPGYP--g

I was able to get my kernel running using the suggested temporary fix:

$ conda remove gcc libgcc

I had the same problem. The issue seems to be that the R kernel in Jupyter was looking at a different location which had an older version of ibstdc++.so.6.

Below steps worked for me (logged in as root, since R and python were installed as root):

cp -fv /usr/local/lib64/libstdc++* /lib64/cd /lib64ln -sfT libstdc++.so.6.0.21 libstdc++.so.6

Explanation:

[root@SERVER ~]# strings /usr/local/lib64/libstdc++.so.6 | grep CXXABI_1.3CXXABI_1.3CXXABI_1.3.1CXXABI_1.3.2CXXABI_1.3.3CXXABI_1.3.4CXXABI_1.3.5CXXABI_1.3.6CXXABI_1.3.7CXXABI_1.3.8CXXABI_1.3.9CXXABI_1.3CXXABI_1.3.2CXXABI_1.3.6CXXABI_1.3.9CXXABI_1.3.1CXXABI_1.3.5CXXABI_1.3.8CXXABI_1.3.4CXXABI_1.3.7CXXABI_1.3.3[root@SERVER ~]# strings /lib64/libstdc++.so.6 | grep CXXABI_1.3CXXABI_1.3CXXABI_1.3.1CXXABI_1.3.2CXXABI_1.3.3CXXABI_1.3.4CXXABI_1.3.5CXXABI_1.3.6CXXABI_1.3.7

We can see that /lib64/libstdc++.so.6 points to an older version than /usr/local/lib64/libstdc++.so.6

[root@SERVER ~]# ls /lib64/libstdc++.so.* -lrt-rwxr-xr-x 1 root root   830776 Mar  5  2015 /lib64/libstdc++.so.5.0.7lrwxrwxrwx 1 root root       18 Apr 29  2016 /lib64/libstdc++.so.5 -> libstdc++.so.5.0.7lrwxrwxrwx 1 root root       19 Jan 27 01:46 /lib64/libstdc++.so.6 -> libstdc++.so.6.0.19-rwxr-xr-x 1 root root 11103508 Feb  3 21:41 /lib64/libstdc++.so.6.0.19-rwxr-xr-x 1 root root 11103508 Feb  3 21:41 /lib64/libstdc++.so.6.0.21-rw-r--r-- 1 root root     2397 Feb  3 21:41 /lib64/libstdc++.so.6.0.21-gdb.py[root@SERVER ~]# ls /usr/local/lib64/libstdc++* -lrt-rwxr-xr-x 1 root root      905 Jun 15  2016 /usr/local/lib64/libstdc++fs.la-rw-r--r-- 1 root root 10964026 Jun 15  2016 /usr/local/lib64/libstdc++fs.a-rwxr-xr-x 1 root root 11103508 Jun 15  2016 /usr/local/lib64/libstdc++.so.6.0.21lrwxrwxrwx 1 root root       19 Jun 15  2016 /usr/local/lib64/libstdc++.so.6 -> libstdc++.so.6.0.21lrwxrwxrwx 1 root root       19 Jun 15  2016 /usr/local/lib64/libstdc++.so -> libstdc++.so.6.0.21-rwxr-xr-x 1 root root      965 Jun 15  2016 /usr/local/lib64/libstdc++.la-rw-r--r-- 1 root root 28847974 Jun 15  2016 /usr/local/lib64/libstdc++.a

So, I copied all libstd++ files from /usr/local/lib64 to /lib64 and then changed the soft link to point to the new version.