In restrospect, I probably should have posted here before opening an issue on GitHub
I believe a recent release of parnotes (rev. 2, https://www.ctan.org/pkg/parnotes) has broken the Bioconductor LATEX Style 2.0.
While a day ago Travis CI was perfectly happy compiling my package (currently hosted on GitHub), the same Travis configuration now returns the following error:
! Package parnotes Error: Cannot use custom definition of \parnotemarkfmt (parnotes) in parnotes rev. 2 or later. Use \theparnotemark (parnotes) and \parnotecusmarkfmt instead.
I can see in your own Style 2.0 vignette that parnotes is one of the LaTeX packages that is loaded and used by this style.
I'll appreciate if you could look into the issue, and update your code to match the new parnotes requirements.
Thank you very much for the great work!