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Cytofkit

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Please be as geeky as possible. Reference, reference, reference.
Also, please note that this is a mixed bag of math-gurus and mathematically challenged, so choose your words wisely :-)
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nkhanbham

Master

Posts: 53

Joined: Wed Feb 25, 2015 3:03 pm

Post Mon Feb 11, 2019 8:01 pm

Re: Cytofkit

If I run the library command - I get the following errors

https://www.hastebin.com/tulawefawo.coffeescript
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dtelad11

Master

Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Mon Feb 11, 2019 9:30 pm

Re: Cytofkit

Could you please try

BiocManager::install("BiocParallel", version = "3.8")

And then library(cytofkit)?
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albertapaul

Participant

Posts: 7

Joined: Tue Oct 30, 2018 4:30 am

Post Tue Feb 12, 2019 4:07 pm

Re: Cytofkit

Hi,

I was able to successfully run cytofkit in R before (2 months ago) with spectral flow data.
Now the Shiny APP does not open after running the analysis although I get excellen pdf files of the data but channels that I did not select are incorporated !
The Shiny App was a great tool.
Why does it not run anymore?
Thank you.
Liesbeth.
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Tue Feb 12, 2019 4:33 pm

Re: Cytofkit

Hi Liesbeth,

What version of cytofkit are you using?

I know that for the Premessa R package normalizer+debarcoder, the Shiny extension has been really unstable. In that case, Federico re-wrote the code to force Shiny to run through a web browser window rather than open the Shiny app window. Since then, it's been a lot more stable.

Maybe something similar has happened here?


Mike
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albertapaul

Participant

Posts: 7

Joined: Tue Oct 30, 2018 4:30 am

Post Tue Feb 12, 2019 4:51 pm

Re: Cytofkit

Hi Mike,

No it is the one from GITHYB
Can you give me directions how and which version to use that works
I work with spectral flow data
Thanks
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Nrosine

Participant

Posts: 3

Joined: Wed Nov 14, 2018 12:20 pm

Post Thu Mar 28, 2019 4:20 pm

Re: Cytofkit

Hello

Same problem for me.
I cannot open the shiny app
I have this error message : Error in as.character(tools:::httpdPort) :
cannot coerce type 'closure' to vector of type 'character'

Do you know how to fix it

Best regards
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sgranjeaud

Master

Posts: 123

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Fri Mar 29, 2019 6:33 pm

Re: Cytofkit

Hi,

I think it would be easier to help if you could you post the result of sessionInfo() in a new issue on github.
https://github.com/JinmiaoChenLab/cytofkit/issues

Best,
Samuel
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