Il kernel Jupyter R si arresta in modo anomalo

Question

Ho appena installato R essentials di Anaconda (con R già installato sul mio computer) per poter utilizzare R in Jupyter.

Ora, quando apro un nuovo notebook R in Jupyter, dopo pochi secondi (senza nemmeno digitare nulla) il kernel si blocca e deve essere riavviato.

L'errore che ottengo sul terminale è

[I 12:30:36.297 NotebookApp] Kernel started: dd5dd612-2c8f-4235-9619-1cf5a46b3e89 

IRkernel::main() Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so': /home/alberto/anaconda3/lib/R/library/rzmq/libs/../../../../libstdc++.so.6: version CXXABI_1.3.8' not found (required by /home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so) Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted [I 12:30:39.299 NotebookApp] KernelRestarter: restarting kernel (1/5) IRkernel::main() Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so': /home/alberto/anaconda3/lib/R/library/rzmq/libs/../../../../libstdc++.so.6: version CXXABI_1.3.8' not found (required by /home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so) Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted [I 12:30:42.309 NotebookApp] KernelRestarter: restarting kernel (2/5) IRkernel::main() Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so': /home/alberto/anaconda3/lib/R/library/rzmq/libs/../../../../libstdc++.so.6: version CXXABI_1.3.8' not found (required by /home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so) Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted [I 12:30:45.315 NotebookApp] KernelRestarter: restarting kernel (3/5) IRkernel::main() Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so': /home/alberto/anaconda3/lib/R/library/rzmq/libs/../../../../libstdc++.so.6: version CXXABI_1.3.8' not found (required by /home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so) Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted [W 12:30:46.485 NotebookApp] Timeout waiting for kernel_info reply from dd5dd612-2c8f-4235-9619-1cf5a46b3e89 [I 12:30:48.322 NotebookApp] KernelRestarter: restarting kernel (4/5) WARNING:root:kernel dd5dd612-2c8f-4235-9619-1cf5a46b3e89 restarted IRkernel::main() Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so': /home/alberto/anaconda3/lib/R/library/rzmq/libs/../../../../libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so) Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted [W 12:30:51.329 NotebookApp] KernelRestarter: restart failed [W 12:30:51.329 NotebookApp] Kernel dd5dd612-2c8f-4235-9619-1cf5a46b3e89 died, removing from map. ERROR:root:kernel dd5dd612-2c8f-4235-9619-1cf5a46b3e89 restarted failed! [W 12:30:51.361 NotebookApp] Kernel deleted before session

Credo che potrebbe essere un problema con le librerie condivise, ma non riesco a capire come risolverlo ...

Answer 1

(TEMP FIX SOLO)

Vedere questa discussione: https://groups.google.com/a/continuum.io/forum/#!topic/conda/nqPfPGYP--g

I wa s in grado di ottenere il mio kernel in esecuzione utilizzando la correzione temporanea suggerito:

$ conda remove gcc libgcc

Answer 2

Ho avuto lo stesso problema. Il problema sembra essere che il kernel R in Jupyter stava cercando in una posizione diversa che aveva una versione precedente di ibstdC++. So.6.

Sotto passi ha lavorato per me (loggati come root, poiché R e pitone sono stati installati come root):

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

Spiegazione:

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

Possiamo vedere che/lib64/libstdC++. punti .so.6 a una versione precedente di /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.5.0.7 
lrwxrwxrwx 1 root root  18 Apr 29 2016 /lib64/libstdc++.so.5 -> libstdc++.so.5.0.7 
lrwxrwxrwx 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.6.0.21 
lrwxrwxrwx 1 root root  19 Jun 15 2016 /usr/local/lib64/libstdc++.so.6 -> libstdc++.so.6.0.21 
lrwxrwxrwx 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 

Così, ho copiato tutti libstd ++ fil es da/usr/local/lib64 a/lib64 e quindi modificato il soft link in modo che punti alla nuova versione.