CRAN packages using texi2dvi in vignettes/Makefile

[jarioksa]

Below an email from CRAN:

This concerns packages

HandTill2001 hsdar maSAE vegan

which do as the subject line says. There are number of problems:

a) texi2dvi need not be present. It is an optional install on
Unix-alikes, and MiKTeX on Windows removed it in late 2015.

b) It might be present and not work. The version in texinfo 6.0 uses
bashisms not in POSIX /bin/sh, and that in 6.1 fails when repeated LaTeX
runs are needed (as in hsdar maSAE vegan).

So your usages need correction. Do consider if the Makefile is needed
at all and whether standard mechanisms could be used. If it is needed,
a construction like

$(R_HOME)/bin/Rscript -e "tools::texi2pdf('name.tex', clean = TRUE)"

is more portable. For vegan, which has a .texi file, texi2pdf is
probably needed for that file and should be in SystemRequirements.

Brian D. Ripley, ripley@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

[jarioksa]

An obvious solution is to remove texi2pdf dependence. Branch https://github.com/vegandevs/vegan/tree/texi2dvi-removal removes Makefile and translates FAQ-vegan.texi to FAQ-vegan.Rmd and uses knitr to build it to a standard .html vignette (but not to .pdf).

Changes to previous behaviour are:

• 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.

[jarioksa]

The following standard R commands work:

news(package="vegan")
vignette("FAQ-vegan", package="vegan")
vignette("decision-vegan", package="vegan")
vignette("intro-vegan", package="vegan")
vignette("diversity-vegan", package="vegan")

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.

[jarioksa]

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.

[jarioksa]

The texi2dvi issue and other anomalies were fixed in 3035e70. The changes can be ported to cran-2.3 and after cherry-picking, we'll release vegan-2.3-4.

[jarioksa]

Closed with the v2.3-4 release.