No NEWS.html is generated, but we only have inst/NEWS.Rd. The html was generated by Makefile that was now dropped.
No FAQ-vegan.pdf is generated, but we only have 'inst/doc/FAQ-vegan.html`.
These changes mean that vegandocs() must be re-structured or reconsidered. The vegandocs() function was originally designed to show non-vignette documentation. Now R has developed and all that documentation may be accessible without having a dedicated vegandocs() function.
The NEWS and FAQ opened in a web browser and the other documents as pdf files in my desktop Linux. The vignette names could not be abbreviated. The only thing missing is partitioning.pdf. We need to find a solution for that, but otherwise I suggest vegandocs() is phased out.
texinfo 6.1 causes problems with R. R has some tricks to circumvent these problems, but vegan fails. The latest texinfo is now in Debian, and Kurt Hornik preferred a quick fix. Moving to .Rmdwill fix this in the main branch, but that conflicts with the cran-2.3 branch, and I made there a q quick fix that only replaces the vignettes/FAQ-vegan.texi with a plain text inst/FAQ-vegan and removes vignettes/Makefile. The fix is available in https://github.com/vegandevs/vegan/tree/issue-%23158-quick-fix. This also means that we shall have vegan 2.3-4. This will be a real minor release: apart from the .texi fix it will only have fixes for linestack labels, simper print and biodiver index 19.