>>>>> 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> 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
>>>>> 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
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