无法访问opencpu中用户帐户下的R程序包 [英] unable to access R packages under user account in opencpu

问题描述

我正在尝试从opencpu访问安装在用户帐户下的R软件包.我可以以该用户身份启动R时看到该软件包已安装:

I am trying to access R packages which were installed under a user's account from opencpu. I can see that the package is installed when I start R as that user:

> installed.packages() 
           Package      LibPath                                         
RLIM       "RLIM"       "/limdata/ali/R/x86_64-pc-linux-gnu-library/3.0"
...
> system('whoami');
ali

但是，当我尝试从opencpu访问该库时，出现错误，表明未找到该软件包:

However, when I try to access the library from opencpu, I get errors indicating the package was not found:

$ curl -L http://<my.server>/ocpu/user/ali/library/RLIM
there is no package called 'RLIM'

In call:
find.package(pkgname, lib.loc = lib.loc)
# from same server, to confirm opencpu is running... 
$ curl -L http://<my.server>/ocpu/library 
base
bitops
boot
brew
...

任何帮助将不胜感激！

Any help would be greatly appreciated!

平台信息:

• 主机:Ubuntu 12.04
• opencpu服务器1.0.4-precise0
• opencpu-lib:1.0.4-precise0
• R版本3.0.2(2013-09-25)-飞盘航行"

推荐答案

您的家庭图书馆似乎不在默认位置/home/ali/.因此，需要一些其他步骤来访问您的软件包.

It seems like your home library is not in the default location of /home/ali/. Therefore some additional steps are needed to access your packages.

首先，默认的安全配置文件不允许OpenCPU访问/limdata/.要验证这确实是问题所在，请查看/var/log/kern.log并搜索包含APPARMOR和DENIED的行.请阅读 PDF中标题为"自定义安全配置文件"的部分.服务器手册.

First of all, the default security profile won't allow OpenCPU to access /limdata/. To verify that this is indeed the problem, have a look at /var/log/kern.log and search for lines containing APPARMOR and DENIED. Please read the section titled Customizing the security profile in the PDF server manual.

要将主库添加到安全配置文件中，请编辑/etc/apparmor.d/opencpu.d/custom并添加以下行:

To add your home library to the security profile, edit /etc/apparmor.d/opencpu.d/custom and add these lines:

/limdata/ r,
/limdata/** mrix,

然后，重新启动apparmor并打开opencpu:

Afterwards, restart apparmor and opencpu:

 sudo service apparmor restart
 sudo service opencpu restart

那应该注意安全性限制.我希望这样做.老实说，我还没有测试主目录位于/home之外的情况，但是我认为，如果正确配置了R_LIBS_USER环境变量，它应该可以工作.如果没有，请告诉我:-)

That should take care of the security restrictions. I hope that will do it; honestly I haven't tested a scenario where the home directory is outside of /home but I think if your R_LIBS_USER environment variable is properly configured, it should work. If not let me know :-)

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