Week # 9 - General Discussion Thread

[UMGCCCFCSR]

This is the Week # 09 - It's Raining Functions! - Discussion Thread.

If you have survived the deluge of functions that broke out this week, and are still curious to discuss more, this is the place for you.

Best-
David

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[A-hedgecock-Flowcore]

My Positron Updated and since then, I'ce noticed my functions don't autocomplete in the quarto doc while they do everywhere else. I've scoured the internet the best I could looking for a soln but I'm stumped.

No autocomplete:

In console:

R file

[DavidRach]

I am encountering this one as well, its likely a bug. You could open an issue over on their page:

https://github.com/posit-dev/positron/issues?page=1

They would want the output of the following from the terminal as well for troubleshooting

quarto check

[A-hedgecock-Flowcore]

Ah okay- I was going crazy lol I'll see if I can later today (crazy day in Core today already)

[A-hedgecock-Flowcore]

Before I submitted an issue. Ther are working on a patch but here is a solution in the meantime: posit-dev/positron#12885

[njjacobs]

Getting stuck at this step: flowGate::gs_apply_gating_strategy(MyGatingSet, gating_strategy = GatingTable)

[DavidRach]

Hey @njjacobs, this looks to be the ggplot2 error. Make sure your ggplot2 is upgraded to at least version 4. And then make sure flowGate is the class fork of the package with the bugfixes (0.99.2), not the regular Bioconductor version.

packageVersion("flowGate")
#remove.packages("")
remotes::install_github("DavidRach/flowGate")

If the above doesn't work, run the following and take a screenshot of the outputs:

Console:

installed.packages()

Terminal tab:

quarto check

[DavidRach]

Alternatively, did you create the GatingTable? (Shown as commented out in the screenshot)

[alexandragabrielaferreira]

Hi!!

I'm getting a error while installing luciernaga:

This error occurred when I used:

remotes::install_github("DavidRach/Luciernaga")

and

remotes::install_github("https://github.com/DavidRach/Luciernaga")

something I can do to fix it?

Thank you!

[alexandragabrielaferreira]

Hi again,
I took the hint from the last warning "package not available for this version of R" and went to check if there was a new version for R and updated it. After that I tried installing again and it ran until the end with no warnings.

Sorry for this and thank you for recommending trying installing a new package.
Best
Gabriela

[DavidRach]

Thanks for following up @alexandragabrielaferreira and documenting. We are approaching the time of year when R (and subsequently Bioconductor) versions/packages end up updating, so version clashes when installing things can be a bit hectic. Best- David

[alexandragabrielaferreira]

Hi again!!!

I guess it's a case of the Mondays on my end 🤦

Another error while trying to run the gating strategy:

This is the error in the console:

I will just continue with the lesson and will come back to this part with manual gating but just wanted to share the error in case you have encountered it before.

ETA: the manual gating is also broken. I'm checking package versions and downloading the version from week 08. And now it works again.

I had version 1.11 installed originally (after updating to R 4.6.0) and that one is broken.

Best

[DavidRach]

My guess is it's the ggcyto/flowGate versions. Bioconductor has not yet updated, so for ggcyto with the ggplot2 bug fixes it would be remotes::install_github "RGLab/ggcyto" and since still no reply from the maintainers "DavidRach/flowGate" for flowGate.

[alexandragabrielaferreira]

Exactly the case, it's working now!

[alexandragabrielaferreira]

Hi again,

for problem 2, I created a new function just for keywords and added new ones to the original code.

I run the code and get the function object, with correct code inside. However, I tried to update it by adding more keywords but the object didn't update.

If I rename the function, a new object function is created with everything inside. And I rename to the original function name that one is updated as well.

I tried clearing objects, refreshing objects and turning positron on and off, but still get the same results ie, positron ignoring my function updates or refusing to create the function object.

Has anyone found this bug before?

[DavidRach]

@alexandragabrielaferreira, can you take a screenshot or post the code to your function below (place four before, and four after to create a GitHub code block).

Is it returning the correct updated returns, and just not updating in the right secondary sidebar metadat viewer? Or did I misunderstand?

Thanks!
David