Callr error when running tar_make() in renv project

[adamaltmejd]

Not sure if this is a bug with targets, callr or renv to be honest, but trying here first.

I have been running in to this error message for a while now at the end of the make process but just ignoring it since everything seems to be working anyways:

Error in dyn.unload(env$.path) :
  shared object '/tmp/RtmpAf1Tsp/callr-client--2e18fe9.so' was not loaded
Calls: <Anonymous> -> <Anonymous> -> dyn.unload

But I also had the setting TAR_MAKE_REPORTER="timestamp" set in my .Renviron and when I removed it tar_make() refuses to run and produces the following error:

Error in if (!enabled) return(FALSE) :
  missing value where TRUE/FALSE needed
Calls: source ... renv_bootstrap_load -> <Anonymous> -> renv_load_rprofile
Traceback (most recent calls last):
17: source(".Rprofile", local = TRUE)
16: withVisible(eval(ei, envir))
15: eval(ei, envir)
14: eval(ei, envir)
13: source("renv/activate.R")
12: withVisible(eval(ei, envir))
11: eval(ei, envir)
10: eval(ei, envir)
 9: local(...)
 8: eval.parent(substitute(eval(quote(expr), envir)))
 7: eval(expr, p)
 6: eval(expr, p)
 5: eval(quote(...), new.env())
 4: eval(quote(...), new.env())
 3: renv_bootstrap_load(project, libpath, version)
 2: renv::load(project)
 1: renv_load_rprofile(project)
Execution halted
Error: callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed
Visit https://books.ropensci.org/targets/debugging.html for debugging advice.

I have no problem starting the session or manually running source("renv/activate.R") so it seems it only relates to the process started by callr. This is confirmed by tar_make(callr_function = NULL) running without problem.

It turns out the issue is somehow related to the setting RENV_CONFIG_USER_PROFILE=TRUE in my .Renviron, but not to the contents of the ~/.Rprofile since the error happens even when ~/.Rprofile is empty. But as long as RENV_CONFIG_USER_PROFILE is set at all (either to TRUE or FALSE) the error shows up. But if I have TAR_MAKE_REPORTER="timestamp", tar_make() runs but the prints the error at the end. What do you think, is it a targets issue or not?

Edit: just realized I get the same error running drake::r_make() in a drake project, so seems less likely its targets related I guess.

[wlandau]

It seems like this issue should be related to your renv configuration rather than targets. To test, you can try activating the renv library from inside a callr process.

callr::r(function() library(tidyverse))

I am betting you will get the similar errors. Although, I cannot explain what TAR_MAKE_REPORTER might have to do with it. Incidentally, I recently deprecated TAR_MAKE_REPORTER in favor of tar_config_get("reporter_make") in the development version.

[adamaltmejd]

Ok some progress! TAR_MAKE_REPORTER actually does not matter at all. The reason I was getting another error (where tar_make() wasn't even running) when TAR_MAKE_REPORTER was set was that renv needs there to be a newline in ~.Renviron after RENV_CONFIG_USER_PROFILE when loaded from within callr. If there is no newline starting R still loads my ~/.Rprofile but tar_make() fails. As before callr::r(function() library(targets)) works though.

If there is a newline and RENV_CONFIG_USER_PROFILE=FALSE everything runs like it should. But with a newline and RENV_CONFIG_USER_PROFILE=TRUE every run of tar_make() (no matter if it builds anything or not) produces an error at the end of the processs. Everything runs through though.

Btw I'm getting the same error both on Mac and Linux.

Error in dyn.unload(env$.path) : 
  shared object '/var/folders/b9/b7hn3x0x7pv_1q51k3xmw6m40000gn/T//RtmpFN9t2P/callr-client--72f7508.so' was not loaded
Calls: <Anonymous> -> <Anonymous> -> dyn.unload

[adamaltmejd]

Here is an repo that should produce the errors: https://github.com/adamaltmejd/renv_callr_targets_error

Clone and run run.sh, should produce both errors.

[wlandau]

Thanks for the reprex, I can reproduce both errors now. With Renviron_error1, I also got an error using just callr and not targets:

> callr::r(function() 1)
Error in get_result(output = out, options) : 
  callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed
Type .Last.error.trace to see where the error occurred
> .Last.error
<callr_status_error in get_result(output = out, options):
 callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed>
> .Last.error.trace

 Stack trace:

 1. callr::r(function() 1)
 2. callr:::get_result(output = out, options)
 3. throw(new_callr_error(output, killmsg))

 x callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed 

Still working on the other one.

[wlandau]

Update: using https://github.com/adamaltmejd/renv_callr_targets_error, I can reproduce both errors with show = TRUE in callr::r(). So I believe targets is not the cause of either error.

First error

Using your first two dotfiles, particularly the ~/.Renviron with no line break:

mv ~/.Renviron ~/.Renviron_old
cp Renviron_error1 ~/.Renviron

mv ~/.Rprofile ~/.Rprofile_old
cp Rprofile_empty ~/.Rprofile

Here is what I see:

> callr::r(function() TRUE, show = TRUE)
Error in if (!enabled) return(FALSE) : 
  missing value where TRUE/FALSE needed
Calls: source ... renv_bootstrap_load -> <Anonymous> -> renv_load_rprofile
Traceback (most recent calls last):
17: source(".Rprofile", local = TRUE)
16: withVisible(eval(ei, envir))
15: eval(ei, envir)
14: eval(ei, envir)
13: source("renv/activate.R")
12: withVisible(eval(ei, envir))
11: eval(ei, envir)
10: eval(ei, envir)
 9: local(...)
 8: eval.parent(substitute(eval(quote(expr), envir)))
 7: eval(expr, p)
 6: eval(expr, p)
 5: eval(quote(...), new.env())
 4: eval(quote(...), new.env())
 3: renv_bootstrap_load(project, libpath, version)
 2: renv::load(project)
 1: renv_load_rprofile(project)
Execution halted
Error in get_result(output = out, options) : 
  callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed
Type .Last.error.trace to see where the error occurred
In addition: Warning message:
could not retrieve available packages for url 'https://Rdatatable.gitlab.io/data.table/bin/macosx/contrib/4.0' 
> .Last.error
<callr_status_error in get_result(output = out, options):
 callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed>
> .Last.error.trace

 Stack trace:

 1. callr::r(function() TRUE, show = TRUE)
 2. callr:::get_result(output = out, options)
 3. throw(new_callr_error(output, killmsg))

 x callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed 

Second error

Using the ~/.Renviron file with the line break at the end:

cp Renviron_error2 ~/.Renviron

Here is what I see:

> callr::r(function() TRUE, show = TRUE)
Error in dyn.unload(env$.path) : 
  shared object '/var/folders/k3/q1f45fsn4_13jbn0742d4zj40000gn/T//Rtmp6xlzNZ/callr-client--4669635.so' was not loaded
Calls: <Anonymous> -> <Anonymous> -> dyn.unload
[1] TRUE

[adamaltmejd]

Thanks for engaging with this. Seems clear its on either callr or renv.