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 internal errors during check produce?
11 messages · Kurt Hornik, Jan Gorecki, Deepayan Sarkar +2 more
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 <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
2 days later
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
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 <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
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
On Tue, Jun 30, 2020 at 1:32 PM Martin Maechler
<maechler at stat.math.ethz.ch> 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
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
<maechler at stat.math.ethz.ch> 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
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
> <maechler at stat.math.ethz.ch> 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
>>
>>
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 <maechler at stat.math.ethz.ch> 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
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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: luke-tierney at uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu