RStudio Cloud will not use Python 3

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1

Hello all - trying to set up a cloud environment for my students who can't seem to get python to play along with R. https://rstudio.cloud/project/724316

I am trying to install the packages for the course into an environment with Python3. Here's what I have tried:

> library(reticulate)
> py_discover_config()
python:         /cloud/project/r-reticulate/bin/python
libpython:      /usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.so
pythonhome:     /usr:/usr
virtualenv:     /cloud/project/r-reticulate/bin/activate_this.py
version:        2.7.12 (default, Nov 12 2018, 14:36:49)  [GCC 5.4.0 20160609]
numpy:          /cloud/project/r-reticulate/local/lib/python2.7/site-packages/numpy
numpy_version:  1.16.5

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

Then I used: use_python("/usr/bin/python3", required = TRUE) - and py_config() to check it was the right version. It was version 3 - so I went and installed all the packages. These apparently went into a reticulate virtual environment based on Python2:

> use_python("/cloud/project/r-reticulate/bin/python")
> py_config()
python:         /cloud/project/r-reticulate/bin/python
libpython:      /usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.so
pythonhome:     /usr:/usr
virtualenv:     /cloud/project/r-reticulate/bin/activate_this.py
version:        2.7.12 (default, Nov 12 2018, 14:36:49)  [GCC 5.4.0 20160609]
numpy:          /cloud/project/r-reticulate/local/lib/python2.7/site-packages/numpy
numpy_version:  1.16.5

python versions found: 
 /cloud/project/r-reticulate/bin/python
 /usr/bin/python
 /usr/bin/python3

So then I tried creating a separate environment that specifically used Python3: virtualenv_create("ANLY_Courses", python = "/usr/bin/python3")

> use_python("/cloud/project/ANLY_Courses/bin/python", required = TRUE)
> py_config()
python:         /cloud/project/ANLY_Courses/bin/python
libpython:      /usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.so
pythonhome:     /usr:/usr
virtualenv:     /cloud/project/ANLY_Courses/bin/activate_this.py
version:        2.7.12 (default, Nov 12 2018, 14:36:49)  [GCC 5.4.0 20160609]
numpy:           [NOT FOUND]

NOTE: Python version was forced by use_python function

But clearly this still defaults to 2. Is there anything I can do here to make it use Python3?

Thanks!

2

I think this is not related to RStudio Cloud but to reticulate package, maybe related to this github issue. Have you tried installing the development version of reticulate?

3

I'll note I've had no issues with reticulate 1.13 on my computer using Python3 and creating virtual environments that use Python3 ... that was with anaconda though.

Here's the error I get when I try to install reticulate from github: (seems like it would take too much memory to compile from other errors I am seeing):

> install_github("rstudio/reticulate")
Downloading GitHub repo rstudio/reticulate@master
✔  checking for file ‘/tmp/RtmpDaHKt5/remotesf77b336ba/rstudio-reticulate-64f685a/DESCRIPTION’ ...
─  preparing ‘reticulate’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘reticulate_1.13.0-9004.tar.gz’
   
Installing package into ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package ‘reticulate’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c event_loop.cpp -o event_loop.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c libpython.cpp -o libpython.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c output.cpp -o output.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c python.cpp -o python.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions.
make: *** [python.o] Error 4
/opt/R/3.6.0/lib/R/etc/Makeconf:176: recipe for target 'python.o' failed
ERROR: compilation failed for package ‘reticulate’
* removing ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/reticulate’
* restoring previous ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/reticulate’
Error: Failed to install 'reticulate' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpDaHKt5/filef76cf5a9df/reticulate_1.13.0-9004.tar.gz’ had non-zero exit status

Unfortunately, I can't find the /usr/share/doc/gcc folder to share that information.

4

Update: I was able to download the reticulate github and build it using devtools. Then I uploaded that into the cloud environment and installed it from the .gz file. Now things appear to be working ok - when I did py_discover_config() it said there wasn't anything installed and asked if I wanted mini conda, so I installed that and went along my way with Python3.

Thanks for the help!

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5

If your question's been answered (even by you!), would you mind choosing a solution? It helps other people see which questions still need help, or find solutions if they have similar problems. Here’s how to do it:

6

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