Error compiling reports to pdf in recent version of RStudio

FredHutch / VISCtemplates

Tools for writing reproducible reports at VISC

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Error compiling reports to pdf in recent version of RStudio #150

Open kelliemac opened 1 month ago

kelliemac commented 1 month ago

visc_report type Rmd fails to compile to pdf using RStudio version 2024.04.0+735 (on MacOS)
Error message: ! LaTeX Error: Lonely \item--perhaps a missing list environment.
Issue is in references section with \bibitem in CSLReferences environment (CSLReferences environment is defined in template.tex in VISCtemplates)
Similar issues have been reported due to clashes between latex packages: https://tex.stackexchange.com/questions/387937/bibentry-with-template-causes-error-lonely-item-perhaps-a-missing-list-enviro

kelliemac commented 1 month ago

issue is resolved by reverting to earlier version of RStudio. moving forward: next steps could be replicating the issue with the generic PT report template from VISCtemplates, then seeing if someone on windows gets the same

kelliemac commented 2 weeks ago

issue is resolved by updating the definition of CSLReferences in template.tex (see https://github.com/FredHutch/VISCtemplates/pull/159) but implications for various users (mac vs. windows, different RStudio and pandoc versions, etc.) are unknown. if you run into this issue, please post here! we have a fix that we can direct you to, but are not yet merging it to the main branch due to uncertainty about these implications