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metrumresearchgroup / bbr

R interface for model and project management
https://metrumresearchgroup.github.io/bbr/
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WK files created by bbr - delete by default? #686

Closed jacobleander closed 1 month ago

jacobleander commented 1 month ago

When running NONMEM in parallel on 'sge' using bbr, there is a bunch of WK_ files created that is not deleted. They are all empty. Maybe the default can be to delete these WK files after NONMEM run is completed?

kyleam commented 1 month ago

@jacobleander Thanks for filing an issue.

What bbi version are you using? The latest bbi (version 3.3.0) should take care of removing these (metrumresearchgroup/bbi#306).

jacobleander commented 1 month ago

Thanks for quick response. I am using 3.2.3 (I have not installed it locally in my project activity). I guess then I use the default version that is installed on my disk (using blueprint 22.09).

kyleam commented 1 month ago

Hmm, the bbi version that ships with 22.09 is 3.1.1:

$ /usr/local/bin/bbi version
v3.1.1
$ echo $METWORX_VERSION
22-09.00.04

Perhaps you've got another installed somewhere on your PATH. which bbi would let you know what's taking precedence in your shell.

If you'd like to try out the latest bbi, you could install under a specific project by invoking this from the R console:

# from top-level of project
bbr::use_bbi("bin/bbi")

And then point the bbr.bbi_exe_path option to it (typically done in the project's .Rprofile):

options("bbr.bbi_exe_path" = file.path(getwd(), "bin", "bbi"))
kyleam commented 1 month ago

By the way, the upcoming Metworx blueprint will ship with the latest bbi.

jacobleander commented 1 month ago

Seems that I must have installed a later version than the default in /usr/local/bin/bbi. My bbi is installed in /data/apps/bbi.

bbr::bbi_version() [1] "3.2.3" Session restored from your saved work on 2024-May-07 23:41:36 UTC (6 hours ago) options("bbr.bbi_exe_path") $bbr.bbi_exe_path [1] "/data/apps/bbi"

kyleam commented 1 month ago

@jacobleander Yes, looks like it. If you want to update the bbi installed at that path, you can call bbr::use_bbi() without any arguments. It defaults to bbr.bbi_exe_path if it's set.

kyleam commented 1 month ago

@jacobleander I'll close this issue, as it should be resolved by the latest bbi, but if you run into any problems once you update, please let us know. Thanks.