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grunwaldlab / effectR

An R package to call oomycete effectors
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System which calls #8

Closed knausb closed 7 years ago

knausb commented 7 years ago

I see

system("which mafft", intern = T)

in the file test_effector_summary.R. I suspect this will not work on Windows.

zachary-foster commented 7 years ago

Yea, I would use Sys.which("mafft") instead. I would also be a good idea to put these calls inside a testthat chunk that starts with a skip_on_cran() call, as is done here:

https://github.com/grunwaldlab/effectR/blob/d72fae3e6a37a93a6ed42d4dceff3d47b616f12a/tests/testthat/test_HMM.R#L22-L31

Otherwise, it will fail when run on CRAN because they will not have mafft installed