Jupyter R 内核崩溃
Jupyter R kernel crashes
为了在 Jupyter 中使用 R，我刚刚从 Anaconda 安装了 R essentials（我的电脑上已经安装了 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
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: versionCXXABI_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: versionCXXABI_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
我想这可能是共享库的问题，但我不知道如何解决...
（仅临时修复）
查看此讨论：https://groups.google.com/a/continuum.io/forum/#!topic/conda/nqPfPGYP--g
我能够使用建议的临时修复程序获得我的内核 运行：
$ conda remove gcc libgcc
我遇到了同样的问题。问题似乎是 Jupyter 中的 R 内核正在查看具有旧版本 ibstdc++.so.6 的不同位置。
以下步骤对我有效（以 root 登录，因为 R 和 python 是作为 root 安装的）：
cp -fv /usr/local/lib64/libstdc++* /lib64/
cd /lib64
ln -sfT libstdc++.so.6.0.21 libstdc++.so.6
解释：
[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 link 更改为指向新版本。
为了在 Jupyter 中使用 R，我刚刚从 Anaconda 安装了 R essentials（我的电脑上已经安装了 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
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: versionCXXABI_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: versionCXXABI_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: versionCXXABI_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
我想这可能是共享库的问题，但我不知道如何解决...
（仅临时修复）
查看此讨论：https://groups.google.com/a/continuum.io/forum/#!topic/conda/nqPfPGYP--g
我能够使用建议的临时修复程序获得我的内核 运行：
$ conda remove gcc libgcc
我遇到了同样的问题。问题似乎是 Jupyter 中的 R 内核正在查看具有旧版本 ibstdc++.so.6 的不同位置。
以下步骤对我有效（以 root 登录，因为 R 和 python 是作为 root 安装的）：
cp -fv /usr/local/lib64/libstdc++* /lib64/
cd /lib64
ln -sfT libstdc++.so.6.0.21 libstdc++.so.6
解释：
[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 link 更改为指向新版本。