FAQ  •  Register  •  Login

Phenograph

Forum rules
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 :-)
<<

ErinSimonds

Master

Posts: 50

Joined: Tue May 13, 2014 8:04 pm

Post Wed Mar 21, 2018 6:01 pm

Re: Phenograph

Hi MIke,

Yeah, installing XCode is a critical step to use the Github version. You will also need XQuartz installed from here. But I don't think either of these will fix the error you're seeing.

It looks like you're running into a compilation error because there was a change in the headers in High Sierra. Others have described the same type of error in other software (example). To get past this error, the authors of cytofkit will need to updaet their code to properly handle High Sierra. If you don't mind, could you please file a bug report on the cytofkit Github page here?

In the meantime, you can try installing from BioConductor. The "random clustering" bug has been squashed in the version of cytofkit currently on BioConductor (1.10.0). Hopefully this will work since it involves pre-compiled binaries for Mac. Install from BioConductor with this code in R:

  Code:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cytofkit")


Let me know if that works!

ES
<<

mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Mar 21, 2018 6:16 pm

Re: Phenograph

Hi Erin,

Thanks for the additional comments. Yes, I'd heard about some High Sierra-related bugs, but didn't realize this would be one of them!

I'll file a bug report on it on the Cytofkit Github. And I was able to get the v1.10.0 Bioconductor installed, and the GUI opens fine. The main reason I wanted the v1.11.3 was to have the direct click to FlowSOM in the GUI, rather than having to do it in the post-analysis section. But that's not a big deal right now.


Thanks for your help,
Mike
<<

mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed May 16, 2018 6:09 pm

Re: Phenograph

Hi Erin and all,

I had posted the issue about High Sierra and the developer Cytofkit (from Github, not Bioconductor).

I heard back from the Cytofkit maintainers:
They recommended checking this Stack Overflow link: https://stackoverflow.com/questions/328 ... igh-sierra


From that link, I saw the bit about [xcode-select --install] being a problem.

So, I opened Terminal, pasted that in, and it did install the Xquartz devtools.

I then had to close Xquartz (it had opened during updating).

After that, I could get the
"Install this development version, use:

if(!require(devtools)){
install.packages("devtools") # If not already installed
}
devtools::install_github("JinmiaoChenLab/cytofkit") "

to work, allowing me to update to Cytofkit v1.11.3


However, when I then opened cytofkit, I got only a tiny blank Shiny window. RStudio locked up, and I had to close both Xquartz (again) and Rstudio.

After that, opening cytofkit, I got the proper Shiny GUI (with the now-clickable FlowSOM option).


So: if anyone else has this problem:
1) Type "xcode-select --install" into Terminal, follow the instructions, close Xquartz down.
2) Then open RStudio, update with the devtools Github Cytofkit (currently v1.11.3).
3) Close Rstudio (and Xquartz again, if necessary).
4) Open Rstudio and launch Cytofkit.....you should now see FlowSOM as a clustering option on the landing GUI.


Thanks to Erin and Cytofkit developers!
Mike
<<

ErinSimonds

Master

Posts: 50

Joined: Tue May 13, 2014 8:04 pm

Post Wed May 16, 2018 6:11 pm

Re: Phenograph

Nice troubleshooting, Mike. Thanks for posting the final solution!

ES
Previous

Return to CyTOF data analysis

Who is online

Users browsing this forum: No registered users and 12 guests