On 18.06.2018 16:38, Marius Hofert wrote:
On Sun, Jun 17, 2018 at 2:13 AM Uwe Ligges
<lig...@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
ad...@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...).
Not sure, Gabor Czardi is a main maintainer of that service, I am sure
he will respond quickly.
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.
Yes, but unfortunately that is not possible for the machines we are
talking about.
Best,
Uwe
Cheers,
M
Best,
Uwe Ligges
Am I missing anything?
Thanks & cheers,
Marius
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