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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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Installing Slingshot with R version 4.0.5 #191

Closed apekshasingh closed 2 years ago

apekshasingh commented 2 years ago

Hi there, thanks so much for your package and timely replies!

I am trying to install slingshot to a server on which the latest version of R I have access to is 4.0.5. This results in the following error "ERROR: dependency ‘TrajectoryUtils’ is not available for package ‘slingshot’". Going back through older issues, I did find this similar problem mentioned here and it seems like there is a workaround? I had a little trouble following your suggestion of modifying and installing the source code for TrajectoryUtils, could you clarify a bit more?

Thank you so much as always!

kstreet13 commented 2 years ago

Hi @apekshasingh,

Ok so, what I was describing there was a very hacky approach that probably shouldn't be used. I think the "correct" approach would be to install the latest version of Bioconductor for which the installation works (3.12? 3.11?). You can install specific versions via BiocManager::install() by setting the version argument.

The (possibly dangerous?) approach I described there was to download the source package from GitHub and manually change the R version listed in the DESCRIPTION file. However, I'm looking at it now and it seems like the DESCRIPTION file no longer explicitly mentions an R version, so you may be able to just download it and install it right away? Or even just install directly from GitHub (via devtools::install_github()). It's always possible that I'm missing something, but that might work for you.

Best, Kelly

apekshasingh commented 2 years ago

Thanks I will try this! Much appreciated as always!