errors generating PDF report

[ftwkoopmans]

Case 1: the R console shows an error that TeX/TinyTex needs to be updated

Recently we've seen the following error on some computers, triggered by updates to R packages/tools used by MS-DAP to create the PDF report.

A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois").
! LaTeX Error: File `bookmark.sty' not found.

! Emergency stop.
<read *>

Error: LaTeX failed to compile report.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See report.log for more info.
Called from: show_latex_error(file, logfile)

solution:

Start a clean RStudio session, then run the following R command:

tinytex::reinstall_tinytex(repository = "illinois")

Case 2: general problems encountered when creating the MS-DAP PDF report

Description

MS-DAP was previously installed and working well; R, RStudio and RTools[windows only] have been installed & MS-DAP R package was installed using R command shown on the MS-DAP GitHub main page. However, now problems occur at the very last step of the MS-DAP pipeline: the PDF report is not created.

Potential cause

This might occur when you update a subset of rmarkdown-related R packages and thus some packages needed by MS-DAP to create the PDF report are outdated or the versions of mutually-dependent packages are out-of-sync.

Example errors

Some example errors that may be shown in the R console;

• quitting from lines N-M report.Rmd
• No output PDF file written
• the function xfun::isFALSE() has been deprecated
• xdvipdfmx:fatal: File ended prematurely
• Segmentation fault (core dumped) 'xelatex' -halt-on-error -interaction=batchmode 'report.tex' > /dev/null 2> '/tmp/Rtmp6q3WSx/stderr164bf7d92f097'

Solution

Various reported issues have been traced back to outdated R packages that are related to knitr/rmarkdown. Please try the following installation steps (in order):

• On Windows, ensure that RTools has been installed (e.g. use the R command pkgbuild::has_rtools() , which should yield TRUE). If RTools is not installed yet (although it should be prior to installing MS-DAP!); close RStudio, visit the website https://cran.r-project.org/bin/windows/Rtools/history.html, download the RTools version matching your R installation (version number is shown in the console when you start RStudio) and install it
• Prior to installing R packages, close (all instances of) RStudio and start a fresh RStudio session (so none of the packages are in use)
• In Rstudio, issue the following commands to ensure each R package needed for MS-DAP's RMarkdown PDF reporting is installed. One by one, run each line of code and verify that installation completed succesfully:
• install.packages("xfun", repos = "https://cloud.r-project.org", type = "source")
• install.packages("knitr", repos = "https://cloud.r-project.org")
• install.packages("rmarkdown", repos = "https://cloud.r-project.org")
• install.packages("tinytex", repos = "https://cloud.r-project.org")
• tinytex::reinstall_tinytex()
• now close and restart RStudio: MS-DAP report generation should work again!

[medsoccer]

Thanks for clarifying as it has been some time since I used the package and just ran into it today after a day of analysis. Is there any way of generating the report without rerunning the analysis?

[ftwkoopmans]

Is there any way of generating the report without rerunning the analysis?

Currently not possible. But you can remove all contrasts using dataset_nostats = remove_contrasts(dataset) to remove all contrasts and store the results in a new dataset object, then use dataset_nostats = analysis_quickstart(dataset_nostats, ...) to generate the QC report without the time-consuming DEA.

For future reference, please create a separate ticket for feature requests or questions that are unrelated to the current issue.