COMBINE-lab/salmon

Conda dependency conflict with ICU between Salmon 1.3.0 and R 4.0.3

Opened this issue · 1 comments

This isn't strictly speaking a bug with salmon per-se, but when installing salmon from conda, its impossible to have both R 4.0.3 and Salmon 1.3.0 installed in the same environment (which is frustrating due to the downstream analysis of Salmon data with wasabi/sleuth then requiring a separate environment).

The core incompatibility seems to be with the International Components for Unicode package. Salmon requires
"icu >=64.2,<65.0a0",
Whereas in one of the R dependencies when installing 4.0.3 in the environment solve the following is specified
"icu >=67.1,<68.0a0",

This seems to be the only conflict I could identify.
This seems to be a new incompatibility introduced with R 4.0.3 and Salmon can coexist alongside R 4.0.2 without issue, so this isn't a huge problem but something I thought should probably be on your radar if it isn't already.

Output from the conda dry-run as follows:
salmon_solve.txt
r-base_solve.txt

rob-p commented

Thanks for the detailed report! I wonder if we can bump the max version on salmon 1.4.0. I seem to remember icu 67 conflicting with another dependency before. We'll have to look into that.