[Rd] R-devel internal errors during check produce?

Jan Gorecki
Mon, 29 Jun 2020 21:34:32 -0000

Thank you both,
You are absolutely correct that example should be minimal, so here it is.

l = list(a=new.env(), b=new.env())
unique(l)

Just for completeness, env_list during check that raises error

env_list <- list(baseenv(),
  as.environment("package:graphics"),
  as.environment("package:stats"),
  as.environment("package:utils"),
  as.environment("package:methods")
)
unique(env_list)

Best regards,
Jan

On Mon, Jun 29, 2020 at 5:42 PM Martin Maechler
<maechler at stat.math.ethz.ch> wrote:
>
> >>>>> Kurt Hornik
> >>>>>     on Mon, 29 Jun 2020 16:13:03 +0200 writes:
>
> >>>>> Jan Gorecki writes:
>     >> So the unique.default is from the R tools package during
>     >> checks.  I don't see those issues on CRAN checks.
>
>     > I cannot reproduce this locally (and have no clues about
>     > docker).  Perhaps you can try to debug this on your end?
>     > And see what env_list is when the error occurs?
>
>     > Best -k
>
> Indeed, if it is a bug in R (as opposed to being an assumption
> that 'data.table' makes about undocumented R internals), it
> should be reproducible with a very small dummy package instead
> of data.table. ... or actually reproducible with relatively
> simple R code calling unique() not envolving any non base package.
>
> Martin
>
>
>     >> Exact environment where I am reproducing this issue is a
>     >> fresh ubuntu, no R packages pre-installed docker pull
>     >> registry.gitlab.com/jangorecki/dockerfiles/r-devel
>     >>
https://gitlab.com/jangorecki/dockerfiles/-/raw/master/r-devel/Dockerfile
>
>     >> On Sat, Jun 27, 2020 at 12:37 AM Jan Gorecki
>     >> <j.gorecki at wit.edu.pl> wrote:
>     >>>
>     >>> Hi R developers,
>     >>>
>     >>> On R-devel (2020-06-24 r78746) I am getting those two
>     >>> new exceptions during R check. I found a change which
>     >>> eventually may be related
>     >>>
https://github.com/wch/r-source/commit/69de92b9fb1b7f2a7c8d1394b8d56050881a5465
>     >>> I think this may be a regression. I grep'ed package
>     >>> manuals and R code for unique.default but don't see
>     >>> any. Usage section of the unique method looks fine as
>     >>> well. Errors look a little bit like internal errors.
>     >>>
>     >>> * checking Rd \usage sections ... NOTE Error in
>     >>> unique.default(env_list) : LENGTH or similar applied to
>     >>> environment object Calls: <Anonymous>
>     >>> ... .get_S3_generics_as_seen_from_package -> unique
->
>     >>> unique.default Execution halted The \usage entries for
>     >>> S3 methods should use the \method markup and not their
>     >>> full name.  * checking S3 generic/method consistency
>     >>> ... WARNING Error in unique.default(env_list) : LENGTH
>     >>> or similar applied to environment object Calls:
>     >>> <Anonymous> ...
.get_S3_generics_as_seen_from_package ->
>     >>> unique -> unique.default
>     >>>
>     >>> I don't think if it is related but I build R-devel
with
>     >>> extra args: --with-recommended-packages
>     >>> --enable-strict-barrier --disable-long-double I check
>     >>> with: --as-cran --no-manual To reproduce download
>     >>> current data.table from CRAN (1.12.8) and run R check
>     >>>
>     >>> Best regards, Jan Gorecki
>
>     >> ______________________________________________
>     >> R-devel at r-project.org mailing list
>     >> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>     > ______________________________________________
>     > R-devel at r-project.org mailing list
>     > https://stat.ethz.ch/mailman/listinfo/r-devel