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FredHutch / VISCtemplates

Tools for writing reproducible reports at VISC
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Create Log Report with PDF/Word template #28

Open wfulp opened 5 years ago

wfulp commented 5 years ago

We want a third output (can be any output; pdf, html,...) that lists all code, messages, warnings, and errors, along with the normal report output.

I'm thinking of adding a adding of trying parameters in the YAML 

params:
  do_log: TRUE
monicagerber commented 4 years ago

Is this still something you want to work on?

wfulp commented 4 years ago

I think we need it eventually for validation purposes. I don't have to be the one to work on it if someone else wants to take the lead.

monicagerber commented 4 years ago

Ok. We can discussing in an upcoming meeting. Thanks!

kelliemac commented 2 months ago

@mayerbry and @asatofh do you think this issue is still relevant?

asatofh commented 2 months ago

@kelliemac Creating a log file that documents when a report was run and includes any errors or warnings was required as part of WI-0010 Analysis Report Documentation and Archiving, but I can't find the specific language anymore. .Rout files are generated when you run R files from the command line, and HVTN figured out a way to do something similar for .Rmd files, but I don't know much about it. Our current not-great practice is to set warning=F if we don't know how to handle the warnings, ideally it would be better to capture these somehow, but I'm not sure how to do it. It's worth revisiting as a conversation, it would be a great practice if we could figure it out..