modified to capture stdout and stderr to log in using system2() being…

[kjsato]

… applicable in Windows as well in flepimop/main_scripts/inference_main.R

Describe your changes.

• use system2() in place of system(), with dir precheck to capture msgs on both stdout and stdout
• modified (assumed) to run in Windows as well
  • Checked okay on WSL2-Windows(ubuntu) of course
• use 'tryCatch'

What does your pull request address? Tag relevant issues.
#169
Mentions of relevant team members.
Please check out whether it works if possible @kimberlynroosa @saraloo

[kjsato]

sorry, I set appropriate persons for reviewers (note that the priority is low)
@kimberlynroosa plz check on MINGW64 environment which you seemed to use

[saraloo]

Thanks Koji. This looks fine to me. Worth double checking @kimberlynroosa if this works for you but I think should be fine!

[TimothyWillard]

@saraloo @kimberlynroosa I'm updating this PR to get it over the finish line since it's been finished. Whenever y'all get a chance could you review/test the changes? Also, I noticed that this PR dumps the log to a subdirectory in model_output instead of in a file in the working directory, does this change in behavior sound correct?

[saraloo]

Thanks tim, I can't test the windows side but it looks right to me. I think not in the subdirectory for consistency would be better? I'm not sure why this was the choice. Fine either way though

[TimothyWillard]

I think not in the subdirectory for consistency would be better? I'm not sure why this was the choice.

This change has been made.