Jupyter R内核崩溃了

Question

我刚从Anaconda安装了R essentials（已经在我的计算机上安装了R），以便在Jupyter中使用R.

现在，当我在Jupyter中打开一个新的R笔记本时，几秒钟后（甚至没有输入任何内容）内核崩溃并需要重新启动。

我在终端上得到的错误是

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

dyn.load中的IRkernel :: main（）错误（文件，DLLpath = DLLpath，...）：无法加载共享对象'/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：版本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未找到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（/home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so要求）调用:: ：... tryCatch - > tryCatchList - > tryCatchOne - >执行暂停[I 12：30：42.309 NotebookApp] KernelResta rter：重启内核（2/5）IRkernel :: main（）dyn.load中的错误（文件，DLLpath = DLLpath，...）：无法加载共享对象'/ 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 ： 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版本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找不到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'（/home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/ libs / stringi.so）调用：:: ... tryCatch - > tryCatchList - > tryCatchOne - >执行暂停[W 12：30：4 6.485 NotebookApp]超时等待来自dd5dd612-2c8f-4235-9619-1cf5a46b3e89的内核_info回复[I 12：30：48.322 NotebookApp] KernelRestarter：重启内核（4/5）警告：root：kernel dd5dd612-2c8f-4235-9619-1cf5a46b3e89重启IRDEnel :: main（）dyn.load中的错误（文件，DLLpath = DLLpath，...）：无法加载共享对象'/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：版本`CXXABI_1.3.8'不是发现（需要/home/alberto/R/x86_64-pc-linux-gnu-library/3.2/stringi/libs/stringi.so）调用：:: ... tryCatch - > tryCatchList - > tryCatchOne - >执行暂停[ W 12：30：51.329 NotebookApp] KernelRestarter：restart failed [W 12：30：51.329 NotebookApp]内核dd5dd612-2c8f-4235-9619-1cf5a46b3e89死亡，从地图中删除。 错误：root：内核dd5dd612-2c8f-4235-9619-1cf5a46b3e89重启失败！ [W 12：30：51.361 NotebookApp]在会话之前删除了内核

我想这可能是共享库的一个问题，但我无法弄清楚如何解决它...

Answer 1

（仅限TEMP FIX）

请参阅此讨论： https ： //groups.google.com/a/continuum.io/forum/#！topic / secondary / nqPfPGYP--g

我能够使用建议的临时修复程序运行我的内核：

$ conda remove gcc libgcc

Answer 2

我有同样的问题。 问题似乎是Jupyter中的R内核正在查看具有旧版ibstdc ++的其他位置.so.6。

以下步骤适用于我（以root身份登录，因为R和python以root用户身份安装）：

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

说明：

[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

我们可以看到/lib64/libstdc++.so.6指向比/usr/local/lib64/libstdc++.so.6更旧的版本

[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

因此，我将所有libstd ++文件从/ usr / local / lib64复制到/ lib64，然后将软链接更改为指向新版本。