Open issues

synapser and Reticulate appear to have a python version issue through PythonEmbedInR
SYNR-1431
Possible to shorten file paths in PythonEmbedInR?
SYNR-1434
synapser error in virtual environment built from Docker
SYNR-1429
Article on Using synapser as a dependency
SYNR-1428
Synapser call to update table fails with error
SYNR-1426
synGetSubmission encounters error
SYNR-1425
Calling arguments by position causes confusing errors
SYNR-1416
Storing a Table: Support Date column types for Synapse DATE Columns
SYNR-1415
Error Cannot find entity with name
SYNR-1413
Set the cache directory directly using synapser
SYNR-1409
Cannot query publicly available fileviews or tables without logging in
SYNR-1407
Link to related documentation about hidden files and how to set-up Config file
SYNR-1399
Consider using function signatures that are R friendly
SYNR-1397
synapser_check build fails on ubuntu
SYNR-1395
Document table objects: PartialRowset, Row, and Rowset
SYNR-1392
synapserutils synToSynapse
SYNR-1390
Document suggested permission for .synapseConfig file
SYNR-1388
synGet of ".zip" file returns it with crazy name (see below)
SYNR-1385
mintDOI wrapper function in R client
SYNR-1369
cannot call 'as.list' on a synapser generator inside of another function
SYNR-1368
synapser requires evaluation ID to be a string instead of an integer
SYNR-1366
improved error message for libffi
SYNR-1358
Need documentation in the vignettes about how to programmatically add versionComment
SYNR-1357
cannot set a versionComment on existing entity
SYNR-1356
synapser::as.data.frame collides with other S4 as.data.frame methods
SYNR-1355
Release SynapseR Client v1.0
SYNR-1352
Activity class requires un-named list for 'used' without any documentation of such behavior
SYNR-1342
legacy client not available for R 3.5
SYNR-1341
PythonEmbedInR should recognize the deprecation syntax
SYNR-1339
The ability to reuse Activity in synapser is broken
SYNR-1330
Use crayon to highlight important output
SYNR-1327
synapser and reticulate don't play nicely
SYNR-1324
Consider replacing PythonEmbedInR dependency with reticulate
SYNR-1310
`synLogin()` with `rememberMe=True` does not work in Rscript
SYNR-1300
Issues with reverting back to older version
SYNR-1299
Investigate user's Python search path on Ubuntu
SYNR-1298
Reconsider terminology for Jenkins machines
SYNR-1294
synapser does not display prompt from the Python client
SYNR-1291
expose 'generateManifest' function
SYNR-1277
Empty list in R is converted to NoneType in Python
SYNR-1272
get('contentSize') method does not work for synapser
SYNR-1262
add to PythonEmbedInR the transformation of Python generators to generator wrapper (with nextElem, etc.)
SYNR-1261
synapser breaks argparse library
SYNR-1253
Set table_query_timeout synapser
SYNR-1252
Should be able to configure a evaluation quota after its been made
SYNR-1242
cannot install on rstudio.cloud
SYNR-1234
explore ability to use other packages for data frame like objects coming from synapser commands
SYNR-1232
Add more examples to .Rd files
SYNR-1206
After ctrl-c, stdout appears to be swallowed
SYNR-1194
File.fileSize isn't mapped correctly from the Python client to synapser
SYNR-1146
issue 1 of 88

synapser and Reticulate appear to have a python version issue through PythonEmbedInR

Description

##Problem
###Originally running embed RMarkdown chunks of python code and bash chunks which source python scripts works but synapser wont load
```{r}
library(synapser)
```
R is already connected to Python!
Error: package or namespace load failed for ‘synapser’:
.onLoad failed in loadNamespace() for 'PythonEmbedInR', details:
call: value[[3L]](cond)
error: ERROR: Missing system dependencies. Please make sure that your machine has the required dependencies listed in the SystemRequirements field of the DESCRIPTION file: https://github.com/Sage-Bionetworks/PythonEmbedInR/blob/master/DESCRIPTION

##After Re-installing PythonEmbedInR and synapser:

  1.  

    1.  

      1. Execute Python Script From CLI/Bash
        ```{bash}
        python foo.py
        ```
        Traceback (most recent call last):
        File "/usr/local/lib/R/site-library/synapser/lib/python3.5/site-packages/site.py", line 73, in <module>
        __boot()
        File "/usr/local/lib/R/site-library/synapser/lib/python3.5/site-packages/site.py", line 3, in __boot
        import os
        ImportError: No module named os

AND

  1.  

    1.  

      1. Python Script Code Chunk
        ```{python}
        import sys
        print("Test python code")
        ```
        Warning in system2(command = python, args = paste0("\"", config_script, :
        running command ''/usr/bin/python' "/usr/local/lib/R/site-library/reticulate/config/config.py" 2>/dev/null' had status 1
        Error in python_config(python_version, required_module, python_versions) :
        Error 1 occurred running /usr/bin/python

Environment

None

Status

Assignee

Bruce Hoff

Reporter

Jake Gockley

Validator

Jake Gockley

Release Version History

None

Components

Sprint

Fix versions

Priority

Critical
Configure