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DillonHammill / CytoExploreR

Interactive Cytometry Data Analysis
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Error occurred during data transformation #194

Open cleanylee opened 7 months ago

cleanylee commented 7 months ago

Error occurred during data transformation, what could be wrong?

GS<- cyto_setup(GS_path) GS<- cyto_transform(GS, type="biex") Error: 'trans' must be a list of transformer objects (generated by scales::trans_new method)

DillonHammill commented 7 months ago

A change was recently made to the scales package which required fixes in flowWorkspace. You will need to update to the latest version from BioC to get the fix:

BiocManager::install("flowWorkspace")
georgersmith99 commented 7 months ago

I updated with: BiocManager::install("flowWorkspace") and am still having the same issue

cleanylee commented 7 months ago

I updated with: BiocManager::install("flowWorkspace") and am still having the same issue

If you are running R on windows like I do, I found some error comes from directory permission issue while updating flowWorkspace. I tried to re-install R and change the default library directory to somewhere else (like "C:\R\"). Now it works for me again.

georgersmith99 commented 7 months ago

Thank you for the help! I gave it a go (albeit on macOS) but unfortunately i get the same response. I don't get an error when updating flowWorkspace it seems.

ChrisSteel-bio commented 6 months ago

@georgersmith99 did you manage to solve this? I'm having the same problem, albeit using ubuntu.

georgersmith99 commented 6 months ago

@georgersmith99 did you manage to solve this? I'm having the same problem, albeit using ubuntu.

unfortunately not, i updated flowWorkspace manually and changed the directory of install and still getting the same issue

ChrisSteel-bio commented 6 months ago

@georgersmith99 After hours of trouble shooting I managed to get it to run by downgrading the scales package.

remove.packages("scales")

remotes::install_version("scales", version = "1.2.0")

Hopefully this can help.

georgersmith99 commented 6 months ago

@georgersmith99 After hours of trouble shooting I managed to get it to run by downgrading the scales package.

remove.packages("scales")

remotes::install_version("scales", version = "1.2.0")

Hopefully this can help.

Yes works for me! Thank you very much!

djhammill commented 6 months ago

Apologies for the delay, I have been away. The fix for the new version of scales hasn't been merged for flowWorkspace as yet, so you will need to install directly from GitHub to get the fix:

devtools::install_github("RGLab/flowWorkspace", ref =  "hotfix/update-according-to-latest-scales-package")

I am working on a fix that will work with both versions of scales.

rebeccaongmtu commented 6 months ago

I downgraded "scales" to v.1.2.0, and tried to reproduce an image from the compensation vignette. Although my code ran, the data didn't transform properly. So you might want to be wary of the data you're generating using this approach and check that it was actually transformed.

What it should look like: Compensation-4

What I get:

image

I'm not able to install the fix. It says:

Error in parse_repo_spec(repo) : 
  Invalid git repo specification: 'RGLab/flowWorkspace/'
LenHC commented 4 months ago

I am having the same issue but the solutions above don't work for me... devtools::install_github("RGLab/flowWorkspace/", ref = "hotfix/update-according-to-latest-scales-package")

I tried this one as well, but I get this error: Error in parse_repo_spec(repo) : Invalid git repo specification: 'RGLab/flowWorkspace/'