R-devel internal errors during check produce?

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R-devel internal errors during check produce?

Jan Gorecki
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

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Re: R-devel internal errors during check produce?

Jan Gorecki
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 <[hidden email]> 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

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Re: R-devel internal errors during check produce?

Kurt Hornik-5
>>>>> 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 <[hidden email]> 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

> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: R-devel internal errors during check produce?

Martin Maechler
>>>>> 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
    >> <[hidden email]> 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

    >> ______________________________________________
    >> [hidden email] mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-devel

    > ______________________________________________
    > [hidden email] mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: R-devel internal errors during check produce?

Jan Gorecki
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
<[hidden email]> 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
>     >> <[hidden email]> 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
>
>     >> ______________________________________________
>     >> [hidden email] mailing list
>     >> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>     > ______________________________________________
>     > [hidden email] mailing list
>     > https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: R-devel internal errors during check produce?

Kurt Hornik-5
>>>>> 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]]
<environment: 0x55695f2f6d20>

[[2]]
<environment: 0x55695f2f6930>

Best
-k


> Best regards,
> Jan

> On Mon, Jun 29, 2020 at 5:42 PM Martin Maechler
> <[hidden email]> 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
>> >> <[hidden email]> 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
>>
>> >> ______________________________________________
>> >> [hidden email] mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> > ______________________________________________
>> > [hidden email] mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: R-devel internal errors during check produce?

Martin Maechler
>>>>> 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]] <environment: 0x55695f2f6d20>

    > [[2]] <environment: 0x55695f2f6930>

    > 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: R-devel internal errors during check produce?

Deepayan Sarkar
On Tue, Jun 30, 2020 at 1:32 PM Martin Maechler
<[hidden email]> 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]] <environment: 0x55695f2f6d20>
>
>     > [[2]] <environment: 0x55695f2f6930>
>
>     > 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: R-devel internal errors during check produce?

Jan Gorecki
In reply to this post by Martin Maechler
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
<[hidden email]> 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]] <environment: 0x55695f2f6d20>
>
>     > [[2]] <environment: 0x55695f2f6930>
>
>     > 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: R-devel internal errors during check produce?

Martin Maechler
>>>>> 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
    > <[hidden email]> 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]] <environment: 0x55695f2f6d20>
    >>
    >> > [[2]] <environment: 0x55695f2f6930>
    >>
    >> > 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: [External] Re: R-devel internal errors during check produce?

luke-tierney
In reply to this post by Jan Gorecki
Thanks. Fixed in R-devel in r78754. This was related to a fix for
PR#17809, not the change to unique.default.

Best,

luke

On Tue, 30 Jun 2020, Jan Gorecki wrote:

> 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
> <[hidden email]> 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]] <environment: 0x55695f2f6d20>
>>
>>    > [[2]] <environment: 0x55695f2f6930>
>>
>>    > 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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--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   [hidden email]
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

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