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JinmiaoChenLab / ezSingleCell2

GNU General Public License v3.0
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Could you please provide the entire folder needed for running Shiny locally #2

Open mumdark opened 1 month ago

mumdark commented 1 month ago

Could you please provide the entire folder needed for running Shiny locally, including subfiles, ui, server, and other necessary files, in a compressed package?

Thanks for your help!

bio1122 commented 1 month ago

I have the same problem .

vd4mmind commented 1 month ago

seems like the https://github.com/JinmiaoChenLab/ezSingleCell2/blob/main/install_R_packages.R is not properly working to install all required libraries for launching the standalone app. Is there any other way to mitigate this problem?

vd4mmind commented 1 month ago

It also seems like there are some dependancy conflicts. Is there locked environment with frozen version that will work or some sort of container?

vd4mmind commented 1 month ago

I did more digging and after running a bunch of test, it seems the main package that fails is FastIntegration and this is majorly failing due to the compilation error ocurring with Rfast. Seems like some of the workarounds are to upgrade the RcppGSL or entirely GSL but this does not seems to be a trivial error at this moment to launch this standalone app. Have been trying to update the GCC but does not resolve entirely. Any workaround would be appreciated else it seems it is difficult to launch standalone ezSingleCell2 in Posit WorkBench under AWS SageMaker.

vd4mmind commented 1 month ago

Here is the final error after updating GCC . It seems this will unfortunately prevail unless anyone has already been able to figure this out with another workaround with version control way of running the dependancies. 

compilation terminated.
/opt/R/4.2.3/lib/R/etc/Makeconf:178: recipe for target 'Coeff.o' failed
make: *** [Coeff.o] Error 1
ERROR: compilation failed for package ‘Rfast’
* removing ‘/home/sagemaker-user/VVDA/Rpackages/Rfast’