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lehner-lab / DiMSum

An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies
MIT License
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graphics issues with r-cairo > 1.5 #18

Open durr1602 opened 9 months ago

durr1602 commented 9 months ago

Hi, Just wanted to let you know that my colleague and I both had trouble with the PNG export of r-cairo (PDF are fine). For me, it meant that every graph (PNG files or the graphs displayed in the html report) had issues with text labels. Specifically, it felt like only a single character could be printed so all characters of the label would overlay on top of one another. I did not have that problem when I was using a past version of dimsum, but lately I've updated to 1.3 and the issue arose.

I tried using this command: conda install -c conda-forge r-cairo>1.5, but it did not solve the problem. I ended up comparing the yml files of both my envs and it turns out the version of r-cairo was 1.15.14 when it worked, 1.16 when it did not work.

Ultimately, using this command: conda install -c conda-forge r-cairo=1.5 (which installed r-cairo 1.15.15) did solve the problem. It'd be good to change the requirements for any new install (if that doesn't cause any other issue, which it doesn't seem to).

Cheers!

andrefaure commented 6 months ago

Thanks for pointing this out @durr1602 ! This is a recurring issue with PNG export in R. Could you clarify the r-cairo version? Was it r-cairo 1.5 or 1.15 that worked? You said the command you used was conda install -c conda-forge r-cairo=1.5 which installed 1.15.15?

durr1602 commented 6 months ago

Woops, that's a typo, sorry. The working version in my env is 1.5.15 (written as 1.5_15 if I run conda list).