[R-pkg-devel] Recommended procedure for solving "Additional issues"?

Marius Hofert m@riu@@hofert @ending from uw@terloo@c@
Mon Jun 18 16:38:22 CEST 2018

On Sun, Jun 17, 2018 at 2:13 AM Uwe Ligges
<ligges using statistik.tu-dortmund.de> wrote:
> On 16.06.2018 21:46, Marius Hofert wrote:
> > Dear DevelopeRs,
> >
> > Is there a recommended procedure for addressing "Additional issues" if
> > they appear on CRAN checks?
> >
> > Say you have some C code in a package which checks fine (Status OK for
> > all flavors) but shows "Additional issues" due to a potential memory
> > problems. One can compile an R version configured with valgrind
> > support and run a corresponding check on the package, but that
> > a) ... sometimes shows false positives (on Mac, for example, as some
> > have reported, see
> > https://stackoverflow.com/questions/29312335/valgrind-on-os-x-yosemite-giving-bogus-errors)
> > b) ... sometimes doesn't provide useful information (at least not in a
> > case I recently ran into).
> > c) Also, one can virtually not always check for all the "Additional
> > issues" that might appear *before* submitting a package to CRAN -- or
> > can one?
> >
> > Concerning c), it would be great if there was a way to 'see' the
> > "Additional issues" *before* submitting to CRAN (like a winbuilder or
> > so). Is there? (I couldn't find anything in WRE). Otherwise, one can
> > do the usual (like --as-cran), hope everything is fine, wait until the
> > CRAN checks are reported, and then, if there are problems, carefully
> > look at the code again, try and find the problem and resubmit in the
> > hope that the problem is fixed => but that's not a good 'procedure' as
> > it creates more work for CRAN etc.
> Well, you can try to run with valgrind and the sanitizers before you
> submit to CRAN yourself.

Hi Uwe,

thanks for helping.

valgrind reported false positives, and 'ASAN' I still struggle with
(setting the flags in ~/.R/Makevars as in WRE led me to some
'Interceptors not working' errors -- might post a question on this
one, not sure if I understood that part correctly).

> Or use R-hub which offers to use  builds with
> enabled sanitizers.

I tried that, thanks for this hint. I got some weird bioconductor
errors (which seem to have nothing to do with my package). I contacted
admin using r-hub.io but didn't get a response yet (don't think that's the
right way to contact them, but found no other way...).

> But you are right, running with valgrind + sanitizers + rchk (protection
> stack imbalance checks) + different BLAS installations is not feasible
> in case you do not suspect problems.
> That is also the reason why CRAN does not always detect these issues in
> the incoming checks, as these checks run only on different specific
> machines in batches.

Would of course be great if we could use exactly the same machines, so
uploading the .tar.gz would reproduce the 'Additional issues' and one
could try that until all issues are resolved (without the need for
local tinkering) before officially submitting a package to CRAN.


> Best,
> Uwe Ligges
> >
> > Am I missing anything?
> >
> > Thanks & cheers,
> > Marius
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >

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