>>>>> 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