issue when using the MongoClient of the PyMongo package

[mlampros]

First of all thank you for the useful package.

I face the following problem when trying to call the MongoClient() module from within an R-session,

reticulate::py_module_available("pymongo")

[1] TRUE

PyMng = reticulate::import("pymongo")

init_pym = PyMng$MongoClient(host = 'localhost', 27017L)

Error: attempt to apply non-function

Normally, I receive this error only if the module is not available, however the PyMongo package is installed in my default python version,

Python 3.5.2 on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pymongo
>>> clt = pymongo.MongoClient(host='localhost:27017')
>>>

> reticulate::py_discover_config(required_module = "pymongo")
python:         /usr/bin/python
libpython:      /usr/lib/python3.5/config-3.5m-x86_64-linux-gnu/libpython3.5.so
pythonhome:     /usr:/usr
version:        3.5.2  [GCC 5.4.0 20160609]
numpy:          /usr/local/lib/python3.5/dist-packages/numpy
numpy_version:  1.12.1
pymongo:        /usr/local/lib/python3.5/dist-packages/pymongo

python versions found: 
 /usr/bin/python
 /usr/bin/python3

I'm also able to open a mongo session and do queries using an ubuntu console,

$ sudo mongod --dbpath /var/lib/mongodb

[sudo] password for lampros: 
2017-07-15T09:39:21.955+0300 I CONTROL  [initandlisten] MongoDB starting : pid=4535 port=27017 dbpath=/var/lib/mongodb 64-bit host=lampros-MS-7640
.....

$ mongo
MongoDB shell version: 3.2.13
connecting to: test
...
>

any ideas, why this error occurs?

[jjallaire]

My best guess is that the mongo library isn't loading due to an LD_LIBRARY_PATH difference between the shell and your R session. Can you provide a traceback associated with the error?

[mlampros]

By enabling debuging (Debug > On Error > Error Inspector ) in Rstudio I receive the following output,

#-------------------------------------------------PYMONGO_reticulate.R
PyMng = reticulate::import("pymongo")
init_pym = PyMng$MongoClient(host = 'localhost', 27017L)   # I added a break point here
#-------------------------------------------------

> debugSource('~/PYMONGO_reticulate.R')
Called from: eval(expr, p)
Browse[1]> n
debug at ~/PYMONGO_reticulate.R#6: init_pym = PyMng$MongoClient(host = "localhost", 27017L)
Browse[2]> n
Error in evalq({ : attempt to apply non-function
> 

The LD_LIBRARY_PATH using the ubuntu console is

$ echo $LD_LIBRARY_PATH
/usr/local/cuda-8.0/lib64:

and from an R session,

> Sys.getenv("LD_LIBRARY_PATH")
[1] "/usr/lib/R/lib::/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/jre/lib/amd64/server"

I even modified the .profile file exporting the paths that appear in the R session, however the error persists.

Thanks for the response.

[jjallaire]

I just tried to reproduce the error locally and couldn't (I can call the PyMng$MongoClient constructor with no errors).

What about if you set options(error = traceback). Does that give us a stack trace that might provide more clues?

[mlampros]

I switched to another Linux OS with the same configuration. The first time I ran

options(error = traceback)
PyMng = reticulate::import("pymongo")
init_pym = PyMng$MongoClient(host = "localhost", 27017L)

I got the following traceback,

Error: attempt to apply non-function
9: stop(e)
8: value[[3L]](cond)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch(loadNamespace(name), error = function(e) stop(e))
4: getNamespace(ns)
3: asNamespace(ns)
2: getExportedValue(pkg, name)
1: reticulate::import

However, since then when I attempt to run the same code I get,

Error: attempt to apply non-function
No traceback available 

a message that I received in my first Linux OS, as well.

Thanks for the response.

[jjallaire]

Okay, I have now reproduce the error when using the CRAN version of reticulate (0.9). The good news is that I can't reproduce using the development version so it must be fixed there! You can install the development version with:

devtools::install_github("rstudio/reticulate")

[mlampros]

yes, using the development version I don't get the error,

PyMng = reticulate::import("pymongo")

init_pym = PyMng$MongoClient('localhost', 27017L)

init_pym

MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True)

thanks a lot for all the responses and for the useful reticulate package.