After updating to the develop branch of stan-math, the make doxygen command now fails. It appears there was a lot of change in config in the last pull request and an update to the 1.8.13 config template. I updated to Doxygen 1.8.13 on my mac and confirmed that’s what’s running.
Are there instructions for how to get doxygen working on a Mac now? I’m still running High Sierra.
Old branches still work with my existing doxygen, but anything after the config change breaks my mac’s doxygen (and also breaks @mitzimorris’s).
Here’s the exact failure:
~/cmdstan/stan/lib/stan_math(feature/0123-complex-var)$ make doxygen
mkdir -p doc/api
doxygen doxygen/doxygen.cfg
warning: the dot tool could not be found at /usr/bin/dot
/Users/carp/cmdstan/stan/lib/stan_math/README.md:4: warning: Unexpected html tag <img> found within <a href=...> context
/Users/carp/cmdstan/stan/lib/stan_math/README.md:8: warning: unable to resolve reference to `https:' for \ref command
I don’t have dot on my path as there’s no hit for which dot.
The errors odd since I turned off the option to make the dot graphs, but maybe on mac it’s doing something odd. I can look into what’s goofing on this today
~/cmdstan/stan/lib/stan_math(feature/0123-complex-var)$ make doxygen
mkdir -p doc/api
doxygen doxygen/doxygen.cfg
warning: the dot tool could not be found at /usr/bin/dot
/Users/carp/cmdstan/stan/lib/stan_math/README.md:4: warning: Unexpected html tag <img> found within <a href=...> context
/Users/carp/cmdstan/stan/lib/stan_math/README.md:8: warning: unable to resolve reference to `https:' for \ref command
interesting, so I built this locally on my mac (OS High Sierra), I got the warnings
doxygen doxygen/doxygen.cfg
warning: the dot tool could not be found at /usr/bin/dot
/Users/wvz764/github/opensource/math/stan/math/opencl/copy.hpp:218: warning: argument 'src' from the argument list of stan::math::copy_cl has multiple @param documentation sections
But also the index.html did compile and the site looks fine locally. For the 2nd warning I looked at copy.hpp and I’m not sure yet what’s causing that warning since that doc comment doesn’t have multiple definitions of @param src
I think I’ve seen the first warning before, for some reason doxygen has a hard time finding dot even if it’s installed in /usr/bin/dot. dot graph generation is turned off tho’ so I’m surprised it’s even trying to connect to dot. lemme play around with this for a minute I’m pretty sure there’s an easy answer
I updated my brew-verse - so now using latest doxygen - 1.8.16.
I tried using doxygen 1.8.13, but that version complained about hrefs in the README.md file.
(at this point, there are so many kobalds gremlins in the system, who knows?)
if you use brew as the installer for graphviz, it puts things in /usr/bin/local, not /usr/bin.
(note: macports might be installing it in /usr/bin )
changing file doxygen.cfg variable DOT_PATH to /usr/bin/local solves that problem.
however, the resulting build in doc/api isn’t finding the stan or eigen directories and/or is not finding the code. what gets built is only the stuff in markdown files.
Some things did get moved around, are you able to see the math namespace like here in the dropdown?
Can you post a screenshot of what your seeing? I’m not sure I understand what boilerplate is in this context (97% of the site’s stuff is boilerplate to me)
Yes my apologies, I think the issue here is the interaction of the two lines above. Since HAVE_DOT is false it should not care about dot, but I think because I set the dot_path it then thinks at some other stage we want dot available
/Users/mitzi/github/stan-dev/cmdstan/stan/lib/stan_math/stan/math/opencl/copy.hpp:184: warning: argument 'src' from the argument list of stan::math::copy_cl has multiple @param documentation sections
