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upset R package compatibility

Open chrisamiller opened this issue 6 years ago • 3 comments

In the R upset package installed in the bioconda/quay repository, the options mainbar.y.label and sets.x.label do not exist, causing a failure:

$ intervene upset --names A,B,C -o . -i $a $b $c

Running UpSet module. Please wait...

Error in upset(fromExpression(expressionInput), nsets = 3, nintersects = 30,  :
  unused arguments (mainbar.y.label = "No. of Intersections", sets.x.label = "Set size")
Execution halted

You are done! Please check your results @ ..
Thank you for using Intervene!

This removes those options, which allows it to proceed

chrisamiller avatar Jan 15 '19 21:01 chrisamiller

Hello @chrisamiller! Please accept my apologies for getting back to you very late. Do you remember what version of R and UpSet package you were using? Thanks!

asntech avatar Oct 19 '19 15:10 asntech

I don't know offhand, but I was running it from the bioconda container, so the environment should be available in that docker image: https://bioconda.github.io/recipes/intervene/README.html

Thanks for looking into it!

chrisamiller avatar Oct 24 '19 18:10 chrisamiller

This seems to be due to the older version of UpSetR. Please check https://github.com/asntech/intervene/issues/38

asntech avatar Oct 14 '20 09:10 asntech