Rui Barradas
2019-Jul-15 12:57 UTC
[Rd] Possible bug in `class<-` when a class-specific '[[.' method is defined
Hello,
Clean R 3.6.1 session on Ubuntu 19.04, RStudio 1.1.453. sessionInfo() at
the end.
I can reproduce this.
counttt <- 0
`[[.MYCLASS` = function(x, ...) {
counttt <<- counttt + 1
# browser()
x = NextMethod()
return(x)
}
df <- as.data.frame(matrix(1:20, nrow=5))
class(df) <- c("MYCLASS","data.frame")
counttt
#[1] 9
But there's more. I tried to print the values of x in the method and got
really strange results
counttt <- 0
`[[.MYCLASS` = function(x, ...) {
counttt <<- counttt + 1
print(x)
# browser()
x = NextMethod()
return(x)
}
df <- as.data.frame(matrix(1:20, nrow=5))
class(df) <- c("MYCLASS","data.frame")
counttt
#[1] 151
If I change print to print.data.frame it goes up to
counttt
#[1] 176
With print.default back to 9. What is the print method called in the
second example?
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 19.04
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0
locale:
[1] LC_CTYPE=pt_PT.UTF-8 LC_NUMERIC=C
[3] LC_TIME=pt_PT.UTF-8 LC_COLLATE=pt_PT.UTF-8
[5] LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8
[7] LC_PAPER=pt_PT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] sos_2.0-0 nlme_3.1-140 matrixStats_0.54.0
[4] fs_1.2.7 xts_0.11-2 usethis_1.5.0
[7] lubridate_1.7.4 devtools_2.0.2 RColorBrewer_1.1-2
[10] rprojroot_1.3-2 rbenchmark_1.0.0 tools_3.6.1
[13] backports_1.1.4 R6_2.4.0 rpart_4.1-15
[16] Hmisc_4.2-0 lazyeval_0.2.2 colorspace_1.4-1
[19] nnet_7.3-12 npsurv_0.4-0 withr_2.1.2
[22] tidyselect_0.2.5 gridExtra_2.3 prettyunits_1.0.2
[25] processx_3.3.0 curl_3.3 compiler_3.6.1
[28] cli_1.1.0 htmlTable_1.13.1 randomNames_1.4-0.0
[31] dvmisc_1.1.3 desc_1.2.0 tseries_0.10-46
[34] scales_1.0.0 checkmate_1.9.1 lmtest_0.9-36
[37] fracdiff_1.4-2 mvtnorm_1.0-10 quadprog_1.5-6
[40] callr_3.2.0 stringr_1.4.0 digest_0.6.18
[43] foreign_0.8-71 rio_0.5.16 base64enc_0.1-3
[46] stocks_1.1.4 pkgconfig_2.0.2 htmltools_0.3.6
[49] sessioninfo_1.1.1 readxl_1.3.1 htmlwidgets_1.3
[52] rlang_0.3.4 TTR_0.23-4 rstudioapi_0.10
[55] quantmod_0.4-14 MLmetrics_1.1.1 zoo_1.8-5
[58] zip_2.0.1 acepack_1.4.1 dplyr_0.8.0.1
[61] car_3.0-2 magrittr_1.5 Formula_1.2-3
[64] Matrix_1.2-17 Rcpp_1.0.1 munsell_0.5.0
[67] abind_1.4-5 stringi_1.4.3 forecast_8.6
[70] yaml_2.2.0 carData_3.0-2 MASS_7.3-51.3
[73] pkgbuild_1.0.3 plyr_1.8.4 grid_3.6.1
[76] parallel_3.6.1 forcats_0.4.0 crayon_1.3.4
[79] lattice_0.20-38 haven_2.1.0 splines_3.6.1
[82] hms_0.4.2 knitr_1.22 ps_1.3.0
[85] pillar_1.4.0 pkgload_1.0.2 urca_1.3-0
[88] glue_1.3.1 lsei_1.2-0 babynames_1.0.0
[91] latticeExtra_0.6-28 data.table_1.12.2 remotes_2.0.4
[94] cellranger_1.1.0 testthat_2.1.0 gtable_0.3.0
[97] purrr_0.3.2 assertthat_0.2.1 ggplot2_3.1.1
[100] openxlsx_4.1.0 xfun_0.6 survey_3.35-1
[103] survival_2.44-1.1 timeDate_3043.102 tibble_2.1.1
[106] memoise_1.1.0 cluster_2.0.8 toOrdinal_1.1-0.0
[109] fitdistrplus_1.0-14 brew_1.0-6
Hope this helps,
Rui Barradas
?s 13:16 de 15/07/19, Duncan Murdoch escreveu:> On 07/07/2019 11:49 a.m., Ghiggi Gionata wrote:
>> Hi all !
>>
>> I noticed a strange behaviour of the function `class<-` when a
>> class-specific '[[.' method is defined.
>>
>> Here below a reproducible example :
>>
>>
>> #-------------------------------------------------------------------.
>>
>> counttt <- 0
>>
>> `[[.MYCLASS` = function(x, ...) {
>> ?? counttt <<- counttt + 1
>> ?? # browser()
>> ?? x = NextMethod()
>> ?? return(x)
>> }
>>
>> df <- as.data.frame(matrix(1:20, nrow=5))
>> class(df) <- c("MYCLASS","data.frame")
>> counttt
>>
>> # The same occurs when using structure(, class=) or
attr(,"class")<-
>> df <- as.data.frame(matrix(1:20, nrow=5))
>> df <- structure(df,
class=c("MYCLASS","data.frame"))
>> attr(df, "class") <-
c("MYCLASS","data.frame")
>>
>> #-------------------------------------------------------------------.
>>
>> Why in this example `class<-` is calling? `[[.MYCLASS` 9 times ?
>>
>> Is there a way to avoid `class<-` to call `[[.MYCLASS` ?
>>
>>
>> Thank you in advance for your help and suggestions.
>
> This is what I see:
>
>
> > counttt <- 0
> >
> > `[[.MYCLASS` = function(x, ...) {
> +?? counttt <<- counttt + 1
> +?? # browser()
> +?? x = NextMethod()
> +?? return(x)
> + }
> >
> > df <- as.data.frame(matrix(1:20, nrow=5))
> > class(df) <- c("MYCLASS","data.frame")
> > counttt
> [1] 0
>
> So there's something else going on in your system.? Maybe post
> sessionInfo()?
>
> Duncan Murdoch
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
Tierney, Luke
2019-Jul-15 13:24 UTC
[Rd] [External] Re: Possible bug in `class<-` when a class-specific '[[.' method is defined
Pasting the entire example into RStudio and hitting return to evaluate does not show this. Evaluating the finall line to print counttt separately does. Looks like RStudio is calling `[[` on your object when examining the environment for the Environment panel. If this concerns you then you should contact RStudio. Best, luke On Mon, 15 Jul 2019, Rui Barradas wrote:> Hello, > > Clean R 3.6.1 session on Ubuntu 19.04, RStudio 1.1.453. sessionInfo() at the > end. > > I can reproduce this. > > counttt <- 0 > > `[[.MYCLASS` = function(x, ...) { > counttt <<- counttt + 1 > # browser() > x = NextMethod() > return(x) > } > > df <- as.data.frame(matrix(1:20, nrow=5)) > class(df) <- c("MYCLASS","data.frame") > counttt > #[1] 9 > > > But there's more. I tried to print the values of x in the method and got > really strange results > > counttt <- 0 > > `[[.MYCLASS` = function(x, ...) { > counttt <<- counttt + 1 > print(x) > # browser() > x = NextMethod() > return(x) > } > > df <- as.data.frame(matrix(1:20, nrow=5)) > class(df) <- c("MYCLASS","data.frame") > counttt > #[1] 151 > > > If I change print to print.data.frame it goes up to > > counttt > #[1] 176 > > With print.default back to 9. What is the print method called in the second > example? > > > sessionInfo() > R version 3.6.1 (2019-07-05) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 19.04 > > Matrix products: default > BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0 > LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0 > > locale: > [1] LC_CTYPE=pt_PT.UTF-8 LC_NUMERIC=C > [3] LC_TIME=pt_PT.UTF-8 LC_COLLATE=pt_PT.UTF-8 > [5] LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8 > [7] LC_PAPER=pt_PT.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > [7] base > > loaded via a namespace (and not attached): > [1] sos_2.0-0 nlme_3.1-140 matrixStats_0.54.0 > [4] fs_1.2.7 xts_0.11-2 usethis_1.5.0 > [7] lubridate_1.7.4 devtools_2.0.2 RColorBrewer_1.1-2 > [10] rprojroot_1.3-2 rbenchmark_1.0.0 tools_3.6.1 > [13] backports_1.1.4 R6_2.4.0 rpart_4.1-15 > [16] Hmisc_4.2-0 lazyeval_0.2.2 colorspace_1.4-1 > [19] nnet_7.3-12 npsurv_0.4-0 withr_2.1.2 > [22] tidyselect_0.2.5 gridExtra_2.3 prettyunits_1.0.2 > [25] processx_3.3.0 curl_3.3 compiler_3.6.1 > [28] cli_1.1.0 htmlTable_1.13.1 randomNames_1.4-0.0 > [31] dvmisc_1.1.3 desc_1.2.0 tseries_0.10-46 > [34] scales_1.0.0 checkmate_1.9.1 lmtest_0.9-36 > [37] fracdiff_1.4-2 mvtnorm_1.0-10 quadprog_1.5-6 > [40] callr_3.2.0 stringr_1.4.0 digest_0.6.18 > [43] foreign_0.8-71 rio_0.5.16 base64enc_0.1-3 > [46] stocks_1.1.4 pkgconfig_2.0.2 htmltools_0.3.6 > [49] sessioninfo_1.1.1 readxl_1.3.1 htmlwidgets_1.3 > [52] rlang_0.3.4 TTR_0.23-4 rstudioapi_0.10 > [55] quantmod_0.4-14 MLmetrics_1.1.1 zoo_1.8-5 > [58] zip_2.0.1 acepack_1.4.1 dplyr_0.8.0.1 > [61] car_3.0-2 magrittr_1.5 Formula_1.2-3 > [64] Matrix_1.2-17 Rcpp_1.0.1 munsell_0.5.0 > [67] abind_1.4-5 stringi_1.4.3 forecast_8.6 > [70] yaml_2.2.0 carData_3.0-2 MASS_7.3-51.3 > [73] pkgbuild_1.0.3 plyr_1.8.4 grid_3.6.1 > [76] parallel_3.6.1 forcats_0.4.0 crayon_1.3.4 > [79] lattice_0.20-38 haven_2.1.0 splines_3.6.1 > [82] hms_0.4.2 knitr_1.22 ps_1.3.0 > [85] pillar_1.4.0 pkgload_1.0.2 urca_1.3-0 > [88] glue_1.3.1 lsei_1.2-0 babynames_1.0.0 > [91] latticeExtra_0.6-28 data.table_1.12.2 remotes_2.0.4 > [94] cellranger_1.1.0 testthat_2.1.0 gtable_0.3.0 > [97] purrr_0.3.2 assertthat_0.2.1 ggplot2_3.1.1 > [100] openxlsx_4.1.0 xfun_0.6 survey_3.35-1 > [103] survival_2.44-1.1 timeDate_3043.102 tibble_2.1.1 > [106] memoise_1.1.0 cluster_2.0.8 toOrdinal_1.1-0.0 > [109] fitdistrplus_1.0-14 brew_1.0-6 > > > > Hope this helps, > > Rui Barradas > > > ?s 13:16 de 15/07/19, Duncan Murdoch escreveu: >> On 07/07/2019 11:49 a.m., Ghiggi Gionata wrote: >>> Hi all ! >>> >>> I noticed a strange behaviour of the function `class<-` when a >>> class-specific '[[.' method is defined. >>> >>> Here below a reproducible example : >>> >>> >>> #-------------------------------------------------------------------. >>> >>> counttt <- 0 >>> >>> `[[.MYCLASS` = function(x, ...) { >>> ?? counttt <<- counttt + 1 >>> ?? # browser() >>> ?? x = NextMethod() >>> ?? return(x) >>> } >>> >>> df <- as.data.frame(matrix(1:20, nrow=5)) >>> class(df) <- c("MYCLASS","data.frame") >>> counttt >>> >>> # The same occurs when using structure(, class=) or attr(,"class")<- >>> df <- as.data.frame(matrix(1:20, nrow=5)) >>> df <- structure(df, class=c("MYCLASS","data.frame")) >>> attr(df, "class") <- c("MYCLASS","data.frame") >>> >>> #-------------------------------------------------------------------. >>> >>> Why in this example `class<-` is calling? `[[.MYCLASS` 9 times ? >>> >>> Is there a way to avoid `class<-` to call `[[.MYCLASS` ? >>> >>> >>> Thank you in advance for your help and suggestions. >> >> This is what I see: >> >> >> > counttt <- 0 >> > >> > `[[.MYCLASS` = function(x, ...) { >> +?? counttt <<- counttt + 1 >> +?? # browser() >> +?? x = NextMethod() >> +?? return(x) >> + } >> > >> > df <- as.data.frame(matrix(1:20, nrow=5)) >> > class(df) <- c("MYCLASS","data.frame") >> > counttt >> [1] 0 >> >> So there's something else going on in your system.? Maybe post >> sessionInfo()? >> >> Duncan Murdoch >> >> ______________________________________________ >> 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 >-- 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
Duncan Murdoch
2019-Jul-15 13:26 UTC
[Rd] Possible bug in `class<-` when a class-specific '[[.' method is defined
On 15/07/2019 8:57 a.m., Rui Barradas wrote:> Hello, > > Clean R 3.6.1 session on Ubuntu 19.04, RStudio 1.1.453. sessionInfo() at > the end.That's not what I'd call a "clean session" with all those packages loaded:> loaded via a namespace (and not attached): > [1] sos_2.0-0 nlme_3.1-140 matrixStats_0.54.0 > [4] fs_1.2.7 xts_0.11-2 usethis_1.5.0 > [7] lubridate_1.7.4 devtools_2.0.2 RColorBrewer_1.1-2 > [10] rprojroot_1.3-2 rbenchmark_1.0.0 tools_3.6.1 > [13] backports_1.1.4 R6_2.4.0 rpart_4.1-15 > [16] Hmisc_4.2-0 lazyeval_0.2.2 colorspace_1.4-1 > [19] nnet_7.3-12 npsurv_0.4-0 withr_2.1.2 > [22] tidyselect_0.2.5 gridExtra_2.3 prettyunits_1.0.2 > [25] processx_3.3.0 curl_3.3 compiler_3.6.1 > [28] cli_1.1.0 htmlTable_1.13.1 randomNames_1.4-0.0 > [31] dvmisc_1.1.3 desc_1.2.0 tseries_0.10-46 > [34] scales_1.0.0 checkmate_1.9.1 lmtest_0.9-36 > [37] fracdiff_1.4-2 mvtnorm_1.0-10 quadprog_1.5-6 > [40] callr_3.2.0 stringr_1.4.0 digest_0.6.18 > [43] foreign_0.8-71 rio_0.5.16 base64enc_0.1-3 > [46] stocks_1.1.4 pkgconfig_2.0.2 htmltools_0.3.6 > [49] sessioninfo_1.1.1 readxl_1.3.1 htmlwidgets_1.3 > [52] rlang_0.3.4 TTR_0.23-4 rstudioapi_0.10 > [55] quantmod_0.4-14 MLmetrics_1.1.1 zoo_1.8-5 > [58] zip_2.0.1 acepack_1.4.1 dplyr_0.8.0.1 > [61] car_3.0-2 magrittr_1.5 Formula_1.2-3 > [64] Matrix_1.2-17 Rcpp_1.0.1 munsell_0.5.0 > [67] abind_1.4-5 stringi_1.4.3 forecast_8.6 > [70] yaml_2.2.0 carData_3.0-2 MASS_7.3-51.3 > [73] pkgbuild_1.0.3 plyr_1.8.4 grid_3.6.1 > [76] parallel_3.6.1 forcats_0.4.0 crayon_1.3.4 > [79] lattice_0.20-38 haven_2.1.0 splines_3.6.1 > [82] hms_0.4.2 knitr_1.22 ps_1.3.0 > [85] pillar_1.4.0 pkgload_1.0.2 urca_1.3-0 > [88] glue_1.3.1 lsei_1.2-0 babynames_1.0.0 > [91] latticeExtra_0.6-28 data.table_1.12.2 remotes_2.0.4 > [94] cellranger_1.1.0 testthat_2.1.0 gtable_0.3.0 > [97] purrr_0.3.2 assertthat_0.2.1 ggplot2_3.1.1 > [100] openxlsx_4.1.0 xfun_0.6 survey_3.35-1 > [103] survival_2.44-1.1 timeDate_3043.102 tibble_2.1.1 > [106] memoise_1.1.0 cluster_2.0.8 toOrdinal_1.1-0.0 > [109] fitdistrplus_1.0-14 brew_1.0-6 > >However, even when I load almost all of those, I don't see the problem. I've got the same R version, and a newer Rstudio version (mine is 1.2.1335 on a Mac). I couldn't load ] "latticeExtradata.table" and "fitdistrplusbrew", and I didn't check my package versions against yours. I'd suspect the issue is with RStudio somehow, because it needs to do a lot to maintain its environment view. Do you see this when running R from the command line? Duncan Murdoch
Duncan Murdoch
2019-Jul-15 13:28 UTC
[Rd] [External] Re: Possible bug in `class<-` when a class-specific '[[.' method is defined
On 15/07/2019 9:24 a.m., Tierney, Luke wrote:> Pasting the entire example into RStudio and hitting return to evaluate > does not show this. Evaluating the finall line to print counttt > separately does. > > Looks like RStudio is calling `[[` on your object when examining the > environment for the Environment panel. If this concerns you then you > should contact RStudio.Now I see it! Duncan Murdoch
Rui Barradas
2019-Jul-15 14:59 UTC
[Rd] Possible bug in `class<-` when a class-specific '[[.' method is defined
Hello, Inline. ?s 14:26 de 15/07/19, Duncan Murdoch escreveu:> On 15/07/2019 8:57 a.m., Rui Barradas wrote: >> Hello, >> >> Clean R 3.6.1 session on Ubuntu 19.04, RStudio 1.1.453. sessionInfo() at >> the end. > > That's not what I'd call a "clean session" with all those packages loaded:You are right, but when I wrote that it *was* clean. Then, for some reason I don't understand, RStudio loaded them all. Guess I'll have to check what is going on here.> >> loaded via a namespace (and not attached): >> ??? [1] sos_2.0-0?????????? nlme_3.1-140??????? matrixStats_0.54.0 >> ??? [4] fs_1.2.7??????????? xts_0.11-2????????? usethis_1.5.0 >> ??? [7] lubridate_1.7.4???? devtools_2.0.2????? RColorBrewer_1.1-2 >> ?? [10] rprojroot_1.3-2???? rbenchmark_1.0.0??? tools_3.6.1 >> ?? [13] backports_1.1.4???? R6_2.4.0??????????? rpart_4.1-15 >> ?? [16] Hmisc_4.2-0???????? lazyeval_0.2.2????? colorspace_1.4-1 >> ?? [19] nnet_7.3-12???????? npsurv_0.4-0??????? withr_2.1.2 >> ?? [22] tidyselect_0.2.5??? gridExtra_2.3?????? prettyunits_1.0.2 >> ?? [25] processx_3.3.0????? curl_3.3??????????? compiler_3.6.1 >> ?? [28] cli_1.1.0?????????? htmlTable_1.13.1??? randomNames_1.4-0.0 >> ?? [31] dvmisc_1.1.3??????? desc_1.2.0????????? tseries_0.10-46 >> ?? [34] scales_1.0.0??????? checkmate_1.9.1???? lmtest_0.9-36 >> ?? [37] fracdiff_1.4-2????? mvtnorm_1.0-10????? quadprog_1.5-6 >> ?? [40] callr_3.2.0???????? stringr_1.4.0?????? digest_0.6.18 >> ?? [43] foreign_0.8-71????? rio_0.5.16????????? base64enc_0.1-3 >> ?? [46] stocks_1.1.4??????? pkgconfig_2.0.2???? htmltools_0.3.6 >> ?? [49] sessioninfo_1.1.1?? readxl_1.3.1??????? htmlwidgets_1.3 >> ?? [52] rlang_0.3.4???????? TTR_0.23-4????????? rstudioapi_0.10 >> ?? [55] quantmod_0.4-14???? MLmetrics_1.1.1???? zoo_1.8-5 >> ?? [58] zip_2.0.1?????????? acepack_1.4.1?????? dplyr_0.8.0.1 >> ?? [61] car_3.0-2?????????? magrittr_1.5??????? Formula_1.2-3 >> ?? [64] Matrix_1.2-17?????? Rcpp_1.0.1????????? munsell_0.5.0 >> ?? [67] abind_1.4-5???????? stringi_1.4.3?????? forecast_8.6 >> ?? [70] yaml_2.2.0????????? carData_3.0-2?????? MASS_7.3-51.3 >> ?? [73] pkgbuild_1.0.3????? plyr_1.8.4????????? grid_3.6.1 >> ?? [76] parallel_3.6.1????? forcats_0.4.0?????? crayon_1.3.4 >> ?? [79] lattice_0.20-38???? haven_2.1.0???????? splines_3.6.1 >> ?? [82] hms_0.4.2?????????? knitr_1.22????????? ps_1.3.0 >> ?? [85] pillar_1.4.0??????? pkgload_1.0.2?????? urca_1.3-0 >> ?? [88] glue_1.3.1????????? lsei_1.2-0????????? babynames_1.0.0 >> ?? [91] latticeExtra_0.6-28 data.table_1.12.2?? remotes_2.0.4 >> ?? [94] cellranger_1.1.0??? testthat_2.1.0????? gtable_0.3.0 >> ?? [97] purrr_0.3.2???????? assertthat_0.2.1??? ggplot2_3.1.1 >> [100] openxlsx_4.1.0????? xfun_0.6??????????? survey_3.35-1 >> [103] survival_2.44-1.1?? timeDate_3043.102?? tibble_2.1.1 >> [106] memoise_1.1.0?????? cluster_2.0.8?????? toOrdinal_1.1-0.0 >> [109] fitdistrplus_1.0-14 brew_1.0-6 >> >> > > However, even when I load almost all of those, I don't see the problem. > I've got the same R version, and a newer Rstudio version (mine is > 1.2.1335 on a Mac).? I couldn't load ] "latticeExtradata.table" and > "fitdistrplusbrew", and I didn't check my package versions against yours. > > I'd suspect the issue is with RStudio somehow, because it needs to do a > lot to maintain its environment view.? Do you see this when running R > from the command line? > > Duncan Murdoch >It's a RStudio thing. Tested with Rscript --vanilla test.R the result is the expected one. (test.R has the obvious contents.) Rui Barradas
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