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greenelab / pdx_exomeseq

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models
MIT License
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VennDiagram version conflict in conda environment #23

Closed gwaybio closed 6 years ago

gwaybio commented 6 years ago

Currently, conda-forge::r-venndiagram=1.6.17 is not compatible with conda-forge::r-gridextra=2.3.

I am updating the feedstock to conda-forge::r-venndiagram=1.6.18 in conda-forge/r-venndiagram-feedstock#2. This issue can be closed once that is tested and merged.

gwaybio commented 6 years ago

the feedstock was merged successfully, but it appears the error goes deeper.

The environment builds successfully, but running Rscript scripts/viz/variant_overlaps.R results in the following error:

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/gway/anaconda3/envs/pdx-exomeseq/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.54: cannot open shared object file: No such file or directory

Based on this error, I added - anaconda::icu=54 to the environment and rebuilt. I then received the following error:

UnsatisfiableError: The following specifications were found to be in conflict:
  - icu 54*
  - plotnine 0.3.0* -> matplotlib >=2.1.0 -> icu >=58.2,<59.0a0

It also appears there is the same hidden conflict between VennDiagram and ggplot2

gwaybio commented 6 years ago

41 replaces the r-venndiagram dependency with matplotlib-venn which removes this error