[Rd] Possible bug in `class<-` when a class-specific '[[.' method is defined

[Duncan Murdoch]

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