Skip to content

Verbose error when site file does not exist #966

@lionel-

Description

@lionel-

Report from https://positpbc.slack.com/archives/C02P4PH94QL/p1763759108177519, copied below:

Users have R_PROFILE_USER="../input/.Rprofile" set in their Renviron.site, and it results in an error in the Positron session that does not show up in the R sessions in Workbench when that file is not found.

The R kernel in Positron is outputting those errors, as I don't see this in R, either inside or outside of an RStudio session. It seems like it should behave similarly to R outside and in RStudio, but it's using a kernel to run R instead.
In strace R outside the product, (no errors shown in the R console):

1201469 09:53:30.595546 openat(AT_FDCWD, "../input/.Rprofile", O_RDONLY) = -1 ENOENT (No such file or directory)

In Rstudio strace output (no errors shown in the R console):

1205030 10:14:46.074706 openat(AT_FDCWD</home/mark>, "../input/.Rprofile", O_RDONLY) = -1 ENOENT (No such file or directory) <0.002210>

In Positron R kernel:

Error in base::sys.source(file = "../input/.Rprofile", envir = <environment>) :
 '../input/.Rprofile' is not an existing file
Error while sourcing R profile file at path '../input/.Rprofile':
Unexpected longjump
Likely caused by:
Error in base::sys.source(file = "../input/.Rprofile", envir = <environment>) :
 '../input/.Rprofile' is not an existing file
> getwd()
[1] "/home/mark"
> file.exists("../input/.Rprofile")
[1] FALSE
> Sys.getenv("R_PROFILE_USER")
[1] "../input/.Rprofile"

And the Positron R kernel logs..

2025-11-21 12:44:44.161 [info] ** Begin kernel log for session R 4.4.2 (r-1715af64) at 11/21/2025, 12:44:35 PM **
Streaming kernel log file: /tmp/kernel-RdwVQj/kernel.log
[R] 2025-11-21T17:44:57.656757Z ERROR Error while sourcing R profile at '../input/.Rprofile': Unexpected longjump
[R] Likely caused by:
[R] Error in base::sys.source(file = "../input/.Rprofile", envir = ) :
[R] '../input/.Rprofile' is not an existing file
[R]
[R]
[R]
[R] R thread backtrace:
[R] 0: 
[R] 1: 
[R] 2: 
[R] 3: 
[R] 4: 
[R] 5: 
[R] 6: 
[R] 7: 
[R] 8: 
[R] 9: 
[R] 10: __libc_start_call_main
[R] at ./csu/../sysdeps/nptl/libc_start_call_main.h:58:16
[R] 11: __libc_start_main_impl
[R] at ./csu/../csu/libc-start.c:360:3
[R] 12: 
[R]
[R] 0: 
[R] 1: 
[R] 2: 
[R] 3: 
[R] 4: 
[R] 5: 
[R] 6: 
[R] 7: 
[R] 8: 
[R] 9: 
[R] 10: __libc_start_call_main
[R] at ./csu/../sysdeps/nptl/libc_start_call_main.h:58:16
[R] 11: __libc_start_main_impl
[R] at ./csu/../csu/libc-start.c:360:3
[R] 12: 
[R]
[R] at crates/ark/src/startup.rs:86
[R]

Metadata

Metadata

Assignees

Labels

No labels
No labels

Type

No type

Projects

No projects

Relationships

None yet

Development

No branches or pull requests

Issue actions