The next major release (version 3.0.0) will offer improved compatibility with newer versions of the reticulate and rjson package.
This release will also include non–backwards compatible changes. Please review the release notes carefully before upgrading, especially if you rely on specific behaviors or APIs from earlier versions.
We maintain the R client to support our R user community, recognizing R as a foundational language in many data workflows. That said, the R client is built on top of the Synapse Python client via the reticulate package. This design allows us to solve complex engineering problems—such as multi-threaded uploads/downloads and file caching—at the Python layer and reuse those solutions in R.
While we aim to provide a reliable R experience, the dependency on Python introduces installation nuances, especially around environment management and package versions. If you encounter issues, we recommend using the Python client directly, which is actively developed and more broadly used.
We appreciate your patience and continued feedback as we work to improve the user experience across both ecosystems.
The synapser package provides an interface to Synapse, a collaborative workspace for reproducible data intensive research projects, providing support for:
The synapser package lets you communicate with the Synapse platform to create collaborative data analysis projects and access data using the R programming language. Other Synapse clients exist for Python, Java, and the web browser.
Note: Since we’re using reticulate 1.28 to interface with the Synapse Python Client synapser is only compatible with Python versions earlier than 3.12. Using Python 3.12 or later may result in errors. We have fully tested and recommend using Python 3.10 for optimal compatibility.
synapser is available as a ready-built package for Microsoft Windows and Mac OSX. For Linux systems, it is available to install from source. Please also check out our System Dependencies article for instructions on how to install system dependencies on Linux environments.
Check out the dedicated install guide for additional instructions
In short you may install synapser via:
For the latest version:
# Install remotes if not already installed
if (!require("remotes", quietly = TRUE)) {
install.packages("remotes")
}
# Install the latest version of synapser (handles compatible dependency versions automatically)
remotes::install_cran("synapser", repos = c("http://ran.synapse.org", "https://cloud.r-project.org"))If you have been asked to validate a release candidate, please use:
remotes::install_cran("synapser", repos = c("http://staging-ran.synapse.org"))If you encounter dependency conflicts (particularly with rjson versions such as namespace ‘rjson’ X.X.X is being loaded, but <= 0.2.21 is required), please see our Troubleshooting vignette for detailed resolution steps.
Important: synapser versions 2.1.0+ require R versions 4.1.3 ≤ R < 4.5. If you are using R ≥ 4.5, the installation will fall back to synapser 2.0.0 instead of the latest version. To use the newest synapser features:
R.version.string in R to see your current versionUnder the hood, synapser uses reticulate and the synapsePythonClient, which is why you are required to have an installation of Python if you don’t already. See instructions below on installing/upgrading Python below.
To get started, try logging into Synapse. If you don’t already have a Synapse account, register here:
Please visit the synapser docs site or view our vignettes for using the synapser package:
browseVignettes(package = "synapser")Knit RMarkdown files to Synapse wikis
Code for managing data coordinating operations (e.g., development of the CSBC/PS-ON Knowledge Portal and individual Center pages) for Sage-supported communities through Synapse.
Download the Python installer from the Official Website of Python here.
Install the Downloaded Python Installer
check Install Python and Check the “Add python.ext to PATH”, then click on the “Install Now” button.
Verify the Update
Note If it still shows the old version, you may restart your system. Or uninstall the old version from the control panel.
Both python 2x and 3x can stay installed in a MAC. Mac comes with python 2x version. To check the default python version in your MAC, open the terminal and type
If you don’t then go ahead and install it with the installer. Go the the python’s official site here.
Now restart the terminal and check again with both commands python —version
Or use to install last version
or write in console >‘R.version.string’ to print out the R version.