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saezlab / liana

LIANA: a LIgand-receptor ANalysis frAmework
https://saezlab.github.io/liana/
GNU General Public License v3.0
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Error in liana_tensor_c2c #110

Closed BenjaminDEMAILLE closed 9 months ago

BenjaminDEMAILLE commented 1 year ago

Hi ! I got :

Error in system2(python.cmd, c("-E", "-c", shQuote("print(1)")), stdout = TRUE, : error in running command

Setting up Conda Environment with Basilisk Error in system2(python.cmd, c("-E", "-c", shQuote("print(1)")), stdout = TRUE, : error in running command

5 | system2(python.cmd, c("-E", "-c", shQuote("print(1)")), stdout = TRUE, stderr = FALSE) 4 | installConda() 3 | obtainEnvironmentPath(env) 2 | basilisk::basiliskStart(liana_env, testload = "scipy.optimize") 1 | liana_tensor_c2c(sce = Bladder_data_sce, score_col = "LRscore", how = "outer", conda_env = NULL)

How can I resolve this @dbdimitrov ?

dbdimitrov commented 1 year ago

Hi,

it seems that you're likely using an outdated version of basilisk. See related issue: https://github.com/LTLA/basilisk/issues/24

Hope this helps.

BenjaminDEMAILLE commented 1 year ago

not really because it's worked on Friday

BenjaminDEMAILLE commented 1 year ago

I'm on Mac M1

BenjaminDEMAILLE commented 1 year ago

this one provoc the bug :

basilisk.utils::installConda() Error in system2(python.cmd, c("-E", "-c", shQuote("print(1)")), stdout = TRUE, : error in running command

same directly in console

I have : v1.11.2 of basilisk.utils

dbdimitrov commented 9 months ago

I hope this was at some point resolved... but we have now provided a way to setup R/Python envrioments for LIANA in this repo: https://github.com/saezlab/ccc_protocols - just in case it proves useful.