Custom R package on OpenCPU / Package found, but no functions visible

问题

CI have written an R package for OpenCPU and want to use it on my own Cloud server. I cannot access any functions even though the package itself is recognized and can be updated, and I can access other (non-custom, e.g. base or stats) packages normally via POST and GET.

I have installed the custom package together with all dependencies to /usr/local/lib/R/site-library and I can use the functions from within an R session locally on the server.

> TestConnectivity
function (x = 100) 
{
    return(sum(rnorm(x)))
}
<environment: namespace:MyPkg>
> TestConnectivity()
[1] 4.174071

The function is exported correctly (documentation using roxygen2):

> getNamespaceExports("MyPkg")
[1] "TestConnectivity"

but when I access it via OpenCPU (either through the browser or through curl) at /ocpu/library/MyPkg/R/TestConnectivity, I get:

object 'TestConnectivity' not found

In call:
get(reqobject, paste("package", reqpackage, sep = ":"), inherits = FALSE)

/ocpu/library/MyPkg/R/ is blank as well (normally, a list of exported functions is expected), but the package itself is visible via browser at /ocpu/library/MyPkg/:

    Information on package 'MyPkg'

Description:

Package:       MyPkg
Description:   in development ...
Type:          Package
Version:       0.1.2
[...]

Index:

TestConnectivity        Test Connectivity of OpenCPU
MyPkg                   Provide R analysis of stored data.
MyPkg-package           Calculation package

I have added its name to the preload field in /etc/opencpu/server.conf, but /ocpu/info only shows it as loaded via a namespace (and not attached): [n] MyPkg_0.1.2. I don't know, if that's a problem.

I also have added access rights to all files necessary for the package's functionality to /etc/apparmor.d/opencpu.d/custom, e.g. the DSN config files for an ODBC database connection.

The package itself consists not only of functions, but also of assembled R6 and S3 class definitions (inheritance within single files) - none of which are used within TestConnectivity(), nevertheless. The functions are also not always placed in files with the exact same name as the function - and sometimes several are combined in one file. (TestConnectivity() is placed within the corresponding TestConnectivity.R file - if it matters.)

Is there some constraint regarding the file structure when using OpenCPU in contrast to using a package locally, which might cause this problem? Or could the class definition files be the cause of the trouble? Any suggestions are appreciated.

回答1:

thanks for the answer (and the great work on OpenCPU, btw...)!

I solved my issue by simply installing the package in /home/myUser/R/3.1/library, e.g. .libPaths()[1] (or R-LIBS-USER[1]) instead of /usr/local/lib/R/site-library.

I got there by incrementally building up a more and more complex test package... and at the point where I nearly had the structure of my actual project, it still worked. Only difference was the installation path.

All in all it's probably an issue with the rights-management on my virtual machine rather than with OpenCPU or my package. I am sorry that I cannot provide more information - if I stumble onto something, I will add it here.

EDIT - I forgot: Of course, the url changes from /ocpu/library/MyPkg/R/ to /ocpu/user/MyUsername/library/MyPkg/R/.

来源：https://stackoverflow.com/questions/25282741/custom-r-package-on-opencpu-package-found-but-no-functions-visible

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package

cloud

opencpu