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Dee-chen / Tree2gd

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Error in plot stage when run Tree2gd_test #16

Open ardy20 opened 1 year ago

ardy20 commented 1 year ago

Dear Sir

I get the following error at plotting stage when I run: Tree2gd_test

Traceback (most recent call last): File "/home/user/miniconda3/bin/Tree2gd", line 8, in sys.exit(main()) File "/home/user/miniconda3/lib/python3.9/site-packages/tree2gd_main.py", line 297, in main run_plot(step6out,args,cf) File "/home/user/miniconda3/lib/python3.9/site-packages/tree2gd/plot.py", line 62, in run_plot file_names = os.listdir("html_plot_in") FileNotFoundError: [Errno 2] No such file or directory: 'html_plot_in'

Dee-chen commented 1 year ago

According to your error, the most likely cause is that the packages required for the R script in step 6 are not loaded correctly. I suggest you eliminate the problem from the following points: 1 Determine the network connection of the server. 2 Jump to the sixth step folder of the test folder and run "Rscript Tree2GD_draw. R" to view the log file. Check whether any packages failed to install or load. If the above conditions exist, you can try to modify the image and download it (the first few lines of Tree2GD_draw. R). 3 If the package is loaded successfully but other errors occur, please send the R log to me to eliminate other errors.

ardy20 commented 1 year ago

Thanks I run Rscript Tree2GD_draw.R

The error Installing package into ‘/opt/R/local/lib’ (as ‘lib’ is unspecified) Warning in install.packages("BiocManager") : 'lib = "/opt/R/local/lib"' is not writable Error in install.packages("BiocManager") : unable to install packages Execution halted

ZaakZoeng commented 2 months ago

Thanks I run Rscript Tree2GD_draw.R

The error Installing package into ‘/opt/R/local/lib’ (as ‘lib’ is unspecified) Warning in install.packages("BiocManager") : 'lib = "/opt/R/local/lib"' is not writable Error in install.packages("BiocManager") : unable to install packages Execution halted

Maybe this link can help you, because I have encountered the same problem before.（https://github.com/Dee-chen/Tree2gd/issues/22）