Error in upgrading rpy2 python package to version 3.3.3

Question

I upgraded my already installed rpy2 package from version 3.2.6 to 3.3.3 and observed the following issue:

Error: C stack usage  454466426436 is too close to the limit
Error: C stack usage  454466426484 is too close to the limit
Error: C stack usage  454466426484 is too close to the limit
Error: bad restore file magic number (file may be corrupted) -- no data loaded
During startup - Warning message:
unable to restore saved data in .RData
Error: C stack usage  454466426372 is too close to the limit
Fatal error: unable to initialize the JIT

When do you get the error? When importing the rpy2 module, or when running some particular code? Which version of R do you have installed? Which OS are you using? — Gorka
– Gorka, Commented May 26, 2020 at 21:32
I get this error when importing rpy2 module. I am using R 3.4.4 on an Linux Ubuntu machine. — Hajar Homayouni
– Hajar Homayouni, Commented May 27, 2020 at 16:03
Is there any .RData file in the working directory? Which is the message that you obtain after renaming it? — Gorka
– Gorka, Commented May 29, 2020 at 21:03

Gorka · Accepted Answer · 2020-05-27 23:56:02Z

1

You should update R to a newer version, at least R-3.6.x, as suggested by the main developer of the package in this issue on Github. I was not able to reproduce your error with the new version R-4.0.0. I hope this fixes your problem.

answered May 27, 2020 at 23:56

Gorka

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