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Bioconductor / basilisk.utils

Clone of the Bioconductor repository for the basilisk.utils package.
https://bioconductor.org/packages/devel/bioc/html/basilisk.utils.html
GNU General Public License v3.0
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fix "error in running command" during conda installation #3

Closed jan-glx closed 3 years ago

jan-glx commented 3 years ago

On my (organization's) machine using basilisk failed with: Error in system2(python.cmd, c("-E", "-c", shQuote("print(1)")), stdout = TRUE, : error in running command (The error message comes from sh and is due to ~ in python.cm not being expanded). Using expand.path fixed it for me (for RELEASE_3_12) I think. (can't tests for master since I am stuck with R/4.0 atm)

LTLA commented 3 years ago

This may already have been fixed in 3.13 and higher. If you follow the daisy chain of calls, dest_path is ultimately generated from getCondaDir(), which itself calls getExternalDir(), which already has a path.expand() statement inside it. It is possible to evade that path.expand() but you would have to be doing something unusual (e.g., specifying your own conda directory).

jan-glx commented 3 years ago

Looks a lot like it, I guess I should have bugged the admins to install R4.1 instead (or tried to install current master (& dir.expiry + ?) outside of bioconductor). I'll close this PR. If anyone else has the same problem they could remotes::install_github("jan-glx/basilisk.utils@RELEASE_3_12") as a workaround.