I recently upgraded my R installation, and I've run into problems when trying to reinstall the Synapser client. The main issue has been installing the "PythonEmbedInR" dependency.
I've resolved some of the issues myself -- installing dependencies such as "wget" and openssl via macports, and manually setting the appropriate symbolic links, but now I'm running into issues with the compiler that are beyond my expertise. I created an issue for this on github, documenting my experience: [https://github.com/Sage-Bionetworks/PythonEmbedInR/issues/107](https://github.com/Sage-Bionetworks/PythonEmbedInR/issues/107). I'm escalating it here because most of the scripts for my dissertation push / pull data from sage, and I'm working towards a deadline. I would welcome any advice from the community.
Brief summary of the current issue:
Configure failed with an error message indicating `g++` could not be found. I updated my "PATH" environment variable to search `/usr/local/gfortran/bin` first. This fixed the first error, but the build still fails. Detailed compiler output is posted in the github issue.
System:
MacBook Pro (16-inch, 2019)
2.3 GHz 8-Core Intel Core i9
running macOS Monterey 12.4
Created by Adam Faranda afaranda Thanks Tom, glad to hear things are back up and running!
Hello @afaranda ,
Apologies for not following up! PythonEmbedInR is indeed deprecated, and we are now using reticulate instead to support synapser. Please follow the installation instructions here: https://github.com/Sage-Bionetworks/synapser. Let me know if you run into any trouble. Hi folks,
I noticed there have been some updates on github for synapser, it looks like PythonEmbedinR is being deprecated. Is synapser now working for R 4.2? Sounds good, thanks for the update. Hi @afaranda ,
Thanks for your continued usage of Synapse. We are still working internally to determine the best path forward with the R client - I will let you know our decision soon. Apologies for the delay and thanks for your patience. Hi Tom, I just wanted to follow up and see what the status of the synapser R client. I had started putting together a wrapper to call Python functions from the Synapse Python Client using reticulate with the same syntax as synapser. It would still take a little bit of work for me to finish it and update my scripts, but I totally understand if the R client is lower priority. Either way, it would be good to know if any updates to the synapser R client were expected in the near future. Thanks again for looking into this. Hi Tom,
Thanks so much for looking into this. I did try Bruce's suggestion, and I can confirm that reticulate + synapseclient seems to be working. Hi @afaranda,
Thanks for your usage of `synapser`. I have commented on the github issue, but I am encountering the same issues you are when trying to update/fix the client. I will be spending more time in trying to provide a fix this week. A note is that currently R version 4.2.0 isn't supported.
Best,
Tom Thanks Bruce, I will investigate that approach and see if I can get it to function -- however a lot of my analysis have use the "synapser" functions heavily, so if there is a way for me to get the R client working that would be best.
I have to say, I've really valued the ability to push and pull data from synapse -- its been very beneficial in terms of organizing my work and tracking analysis provenance. It may be as simple as pointing R to the correct compiler, but we'll see what Thomas thinks.
@afaranda , sorry you have been having difficulties. Linking in @thomas.yu who has been supporting the Synapse client packages (in various languages). One approach some have taken is, rather than using synapser instead to use the [reticulate](https://rstudio.github.io/reticulate/) package along with the [Synapse Python client](https://python-docs.synapse.org/build/html/index.html). Would that approach work for you?
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