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RMINC is not being installed #25
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What's the right way to do this properly? R is just an admin's nightmare at getting things properly installed. |
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That will not install dependencies. |
yes it will. For some reason
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Okay, so we're back to what I'm doing, that's equivalent to dependencies=TRUE. It seems it doesn't accept the "repo =" option, even though the docs say that will be passed forward into the install command. I'm now testing a version where I set the global R repo option instead. |
As a side question, how the heck do I force R to error on any failure, instead of continuing on in the script, making debugging incredibly difficult? |
I think using Rscript instead of R will work this way. |
Is this helpful? |
RMINC has to come from github, it's not on CRAN. That's why that is failing. Dependencies = TRUE is the default as far as I know, you really need the "Suggests" |
And yeah, don't use |
The original line of code is using install_url pointing to the release tarball on github. I think the main issue here is that the R script always succeeds and never stops on error so I don't even know it went wrong. I'll try Rscript -e |
Current failure mode:
And Rscript happily continues on, and exits successfully. So, again I have a VM build without RMINC. |
Well that's a pain,
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Worth a bug report to |
Ehhh, returning the success state of the install is valid. I wonder if it has a strictness argument... |
After much hackery, it finally works and builds again. Still doesn't throw errors when R goes bad, even after wrapping things and upgrading warnings to errors. I'll just have to be very careful reading the logs. |
https://github.com/CobraLab/MINC-VM/blob/master/provision.sh#L165 This isn't quite right I don't think. It doesn't throw a warning when it fails, it just returns stopifnot(
install_url("$RMINC", dependencies=TRUE, upgrade_dependencies=FALSE)
) or if you want a more descriptive error r <- install_url("$RMINC", dependencies=TRUE, upgrade_dependencies=FALSE)
if(!r) stop("Failed to install RMINC") |
I based the wrapping on https://stackoverflow.com/a/26245048/4130016. Maybe I should wrap that again with stopifnot as well? |
that is for That SO answer is bad for other reasons too, |
Am I doing something wrong?
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nevermind... unbalanced parenthesis... |
that's usually the source of unexpected symbol, pleased it's working now 🙂 |
as it's not available via https://cloud.r-project.org/ and so this code fails silently.
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