Changes to CRAN submissions process

Interfaces RStan
1

Heads up for any R package developers using Stan:

The auto-check found additional issues for the last version released on CRAN:
ATLAS https://www.stats.ox.ac.uk/pub/bdr/Rblas/ATLAS/bayesImageS.out
CRAN incoming checks do not test for these additional issues, hence please reply-all and explain:
Have these been fixed?

This is a huge file, but the interesting part is at the very end:

In file included from /data/gannet/ripley/R/test-3.6/StanHeaders/include/stan/math/rev/core.hpp:44,
             from /data/gannet/ripley/R/test-3.6/StanHeaders/include/stan/math/rev/mat.hpp:4,
             from /data/gannet/ripley/R/test-3.6/StanHeaders/include/stan/math.hpp:4,
             from /data/gannet/ripley/R/test-3.6/StanHeaders/include/src/stan/model/model_header.hpp:4,
             from file6f957905b1ec.cpp:8:

/data/gannet/ripley/R/test-3.6/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
/data/gannet/ripley/R/test-3.6/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:17: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
static void set_zero_all_adjoints() {
^~~~~~~~~~~~~~~~~~~~~
Quitting from lines 181-203 (PFAB.Rmd)
Error: processing vignette ‘PFAB.Rmd’ failed with diagnostics:
subscript out of bounds
Execution halted

  • checking PDF version of manual … OK
  • DONE

Status: 1 WARNING

2

Source code is available here: https://bitbucket.org/Azeari/bayesimages/src/v0.5-2/vignettes/PFAB.Rmd

3

That isn’t the interesting part; that is just a bunch of harmless compiler warnings. The error is actually indicated at

Quitting from lines 181-203 (PFAB.Rmd)
Error: processing vignette ‘PFAB.Rmd’ failed with diagnostics:
subscript out of bounds
Execution halted