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hsigeman / findZX

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conflict in the .libPaths of R #6

Open zhuangfjnu opened 2 years ago

zhuangfjnu commented 2 years ago

When I run the plotting job, some package is conflict to my default R version.

Warning message: no DISPLAY variable so Tk is not available Warning message: package 'ggplot2' was built under R version 4.1.0 Loading required package: scales Warning message: package 'scales' was built under R version 4.1.0 Warning message: package 'cowplot' was built under R version 4.1.0 Warning message: package 'viridisLite' was built under R version 4.1.0

Solution:

Edit the ./workflow/scripts/plot_windows.R and plot_windows_linear.R add the .libPaths("./.snakemake/conda/7e994e3adfe76ac9c4a2c1198b96ef3a/lib/R/library")

Solve this conflict.

Zhen

hsigeman commented 2 years ago

Hi Zhen,

That is a possible solution, thanks! The problem is that the path to the conda environment will differ between users. For example, on my system the R libraries are installed here: ".snakemake/conda/154ef20f71f6c17392e550ec37758479/lib/R/library/".

Are the findZX output plots generated despite these warning messages?

Hanna

zhuangfjnu commented 2 years ago

Are the findZX output plots generated despite these warning messages?

The ploting files are not generated, so I notice these warning messages and add the .libPaths define code.