Re: [Rd] R-devel internal errors during check produce?
> Jan Gorecki
> on Tue, 30 Jun 2020 11:29:24 +0100 writes:
> No packages are being loaded, or even installed.
> Did you try running the example on R-devel built with flags I have
> provided in this email?
> I checked now and it is required to use --enable-strict-barrier to
> reproduce the issue.
No, I (and Kurt probably, too) had overlooked the extra flags
setting you'd used
Thank you and Deepayan for checking more there.
I now agree this is something we (R Core) should address one way
or the other.
Martin
> On Tue, Jun 30, 2020 at 9:02 AM Martin Maechler
> wrote:
>>
>> > Kurt Hornik
>> > on Tue, 30 Jun 2020 06:20:57 +0200 writes:
>>
>> > Jan Gorecki writes:
>> >> 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)
>>
>> > Thanks ... but the above work fine for me. E.g.,
>>
R> l = list(a=new.env(), b=new.env())
R> unique(l)
>> > [[1]]
>>
>> > [[2]]
>>
>> > Best -k
>>
>> Ditto here; also your (Jan) 2nd example works fine.
>>
>> So, you must have loaded some (untidy) packages / code which redefine
>> standard base R behavior ?
>>
>> Martin
>>
>>
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Re: [Rd] R-devel internal errors during check produce?
No packages are being loaded, or even installed.
Did you try running the example on R-devel built with flags I have
provided in this email?
I checked now and it is required to use --enable-strict-barrier to
reproduce the issue.
On Tue, Jun 30, 2020 at 9:02 AM Martin Maechler
wrote:
>
> > Kurt Hornik
> > on Tue, 30 Jun 2020 06:20:57 +0200 writes:
>
> > Jan Gorecki writes:
> >> 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)
>
> > Thanks ... but the above work fine for me. E.g.,
>
> R> l = list(a=new.env(), b=new.env())
> R> unique(l)
> > [[1]]
>
> > [[2]]
>
> > Best -k
>
> Ditto here; also your (Jan) 2nd example works fine.
>
> So, you must have loaded some (untidy) packages / code which redefine
> standard base R behavior ?
>
> Martin
>
>
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Re: [Rd] R-devel internal errors during check produce?
On Tue, Jun 30, 2020 at 1:32 PM Martin Maechler
wrote:
>
> > Kurt Hornik
> > on Tue, 30 Jun 2020 06:20:57 +0200 writes:
>
> > Jan Gorecki writes:
> >> 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)
>
> > Thanks ... but the above work fine for me. E.g.,
>
> R> l = list(a=new.env(), b=new.env())
> R> unique(l)
> > [[1]]
>
> > [[2]]
>
> > Best -k
>
> Ditto here; also your (Jan) 2nd example works fine.
>
> So, you must have loaded some (untidy) packages / code which redefine
> standard base R behavior ?
Looking inside Jan's Dockerfile, it turns out that he is configuring R with
./configure --with-recommended-packages --enable-strict-barrier
--disable-long-double
and with that I can reproduce:
> unique(list(new.env()))
Error in unique.default(list(new.env())) :
LENGTH or similar applied to environment object
--enable-strict-barrier is enough to reproduce the error.
-Deepayan
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Re: [Rd] R-devel internal errors during check produce?
> Kurt Hornik
> on Tue, 30 Jun 2020 06:20:57 +0200 writes:
> Jan Gorecki writes:
>> 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)
> Thanks ... but the above work fine for me. E.g.,
R> l = list(a=new.env(), b=new.env())
R> unique(l)
> [[1]]
> [[2]]
> Best -k
Ditto here; also your (Jan) 2nd example works fine.
So, you must have loaded some (untidy) packages / code which redefine
standard base R behavior ?
Martin
__
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Re: [Rd] R-devel internal errors during check produce?
> Jan Gorecki writes:
> 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)
Thanks ... but the above work fine for me. E.g.,
R> l = list(a=new.env(), b=new.env())
R> unique(l)
[[1]]
[[2]]
Best
-k
> Best regards,
> Jan
> On Mon, Jun 29, 2020 at 5:42 PM Martin Maechler
> 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
>> >> 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:
>> >>> ... .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:
>> >>> ... .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@r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> > __
>> > R-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] R-devel internal errors during check produce?
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
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
> >> 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:
> >>> ... .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:
> >>> ... .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@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] R-devel internal errors during check produce?
> 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 >> 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: >>> ... .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: >>> ... .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@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel internal errors during check produce?
> 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 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: ... .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: ... .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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel internal errors during check produce?
So the unique.default is from the R tools package during checks. I don't see those issues on CRAN checks. 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 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: ... .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: ... .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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
