[R-pkg-devel] rhub, docker and Bioconductor

[Ivan Krylov]

On Tue, 7 Jan 2020 13:54:38 +0000
Christian Martin Hennig <christian.hennig using unibo.it> wrote:

> Are there any other options apart from rhub/docker to get wiser about
> my errors and issues (error on debian-clang in a routine that shows
> nothing suspicious on my machine

I cannot answer your original questions, but I can offer some advice on
the problems uncovered by package checks:

> covinv <- try(solve(m))
> if (class(covinv) != "try-error")

In R-devel, matrices are now also arrays [*]:

>> matrix objects now also inherit from class "array", namely, e.g.,
>> class(diag(1)) is c("matrix", "array") which invalidates code
>> assuming that length(class(obj)) == 1, an incorrect assumption that
>> is less frequently fulfilled now.

Use !inherits(convinv, 'try-error') instead.

> additional issues
> ATLAS<https://www.stats.ox.ac.uk/pub/bdr/Rblas/ATLAS/fpc.out>
> MKL<https://www.stats.ox.ac.uk/pub/bdr/Rblas/MKL/fpc.out>
> noLD<https://www.stats.ox.ac.uk/pub/bdr/noLD/fpc.out>
> OpenBLAS)?<https://www.stats.ox.ac.uk/pub/bdr/Rblas/OpenBLAS/fpc.out>

These mostly seem to be concerned with the package startup message from
the mclust package. Try wrapping the calls to library(mclust) into
suppressPackageStartupMessages()?

As for the numbers being different between .Rout.save and actual test
results in ATLAS/MKL/noLD/OpenBLAS tests despite set.seed() being used,
I am not sure what could be done. RNGversion() might help, but this
could also be caused by differences in mclust version, in which case
the result might just be impossible to reproduce.

-- 
Best regards,
Ivan

[*] https://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html
Link should be valid until R-4.0.0 is released.