[Bug]: qenv is valid but code is not reproducible
Nadie ha tomado este issue todavía.
Evaluación
- Dificultad
- 4/5
- Tiempo estimado
- 3-5 días
- Aptitud para principiantes
- 38/100
Línea de trabajo
Reproduce los ejemplos de within(qenv(), ...) en una sesión nueva de R --vanilla y, después, inspecciona la inicialización de qenv y el uso de .GlobalEnv. Compara el comportamiento cuando teal.modules.clinical está cargado frente a cuando está ausente; el trabajo debería considerarse terminado cuando se impida que un qenv parezca válido si su código depende de objetos o funciones no disponibles.
Escrito por el modelo de indexación a partir del texto del issue.
Descripción
What happened?
When creating/modifying a qenv object or derivative, it fails if there are objects or calls to packages outside the environment.
However, when a library is loaded before the creation of the qenv object, functions or object can be found so the code succeeds and results in a valid object even if code results on not reproducible.
This results on teal applications that work, but when users copy and paste the code on a new vanilla R session (R --vanilla), the code will raise an error because there aren't some objects or functions in the environment.
Some testing might also fail as in that environment(s) libraries might not be loaded (as I found on https://github.com/insightsengineering/coredev-tasks/issues/536) .
library("teal.code")
within(qenv(), {ADSL <- tmc_ex_adsl})
#> <qenv.error: object 'tmc_ex_adsl' not found
#> when evaluating qenv code:
#> ADSL <- tmc_ex_adsl>
library("teal.modules.clinical")
#> Loading required package: teal
#> Loading required package: shiny
#> Loading required package: teal.slice
#> Registered S3 method overwritten by 'teal':
#> method from
#> c.teal_slices teal.slice
#>
#> You are using teal version 1.0.0
#>
#> Attaching package: 'teal'
#> The following objects are masked from 'package:teal.slice':
#>
#> as.teal_slices, teal_slices
#> Loading required package: teal.transform
#> Loading required package: tern
#> Loading required package: rtables
#> Loading required package: formatters
#>
#> Attaching package: 'formatters'
#> The following object is masked from 'package:base':
#>
#> %||%
#> Loading required package: magrittr
#>
#> Attaching package: 'rtables'
#> The following object is masked from 'package:utils':
#>
#> str
#> Registered S3 method overwritten by 'tern':
#> method from
#> tidy.glm broom
within(qenv(), {ADSL <- tmc_ex_adsl})
#> <environment: 0x000001dc3ac0c8d0> 🔒
#> Parent: <environment: package:teal.modules.clinical>
#> Bindings:
#> - ADSL: [tbl_df]
Created on 2025-09-09 with reprex v2.1.1
I would expect that the last object don't succeed as the code can't be run in a fresh R session without the teal.modules.clinical package, and often there is no information about it (except in some occasions via parent.env([email protected]) and the attr(env, "name")).
I think this is because the package uses the global environment instead of the base environment on initialization.
This might be related to #201
sessionInfo()
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=Spanish_Spain.utf8 LC_CTYPE=Spanish_Spain.utf8
[3] LC_MONETARY=Spanish_Spain.utf8 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.utf8
time zone: Europe/Madrid
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] teal.modules.clinical_0.11.1 tern_0.9.9
[3] rtables_0.6.13 magrittr_2.0.3
[5] formatters_0.5.11 teal.transform_0.7.0
[7] teal_1.0.0 teal.slice_0.7.0
[9] teal.data_0.8.0 shiny_1.11.1
[11] teal.code_0.7.0 pkgdown_2.1.3
[13] devtools_2.4.5 usethis_3.2.0
loaded via a namespace (and not attached):
[1] gtable_0.3.6 ggplot2_3.5.2 htmlwidgets_1.6.4 remotes_2.5.0.9000
[5] lattice_0.22-7 vctrs_0.6.5 tools_4.5.1 Rdpack_2.6.4
[9] generics_0.1.4 tibble_3.3.0 pkgconfig_2.0.3 Matrix_1.7-4
[13] checkmate_2.3.3 RColorBrewer_1.1-3 lifecycle_1.0.4 compiler_4.5.1
[17] farver_2.1.2 textshaping_1.0.3 httpuv_1.6.16 htmltools_0.5.8.1
[21] later_1.4.4 pillar_1.11.0 urlchecker_1.0.1 tidyr_1.3.1
[25] ellipsis_0.3.2 cachem_1.1.0 sessioninfo_1.2.3 mime_0.13
[29] nestcolor_0.1.3 tidyselect_1.2.1 digest_0.6.37 stringi_1.8.7
[33] dplyr_1.1.4 purrr_1.1.0 splines_4.5.1 fastmap_1.2.0
[37] grid_4.5.1 cli_3.6.5 logger_0.4.0 bsicons_0.1.2
[41] survival_3.8-3 pkgbuild_1.4.8 broom_1.0.9 rutils_0.0.2.92
[45] scales_1.4.0 promises_1.3.3 backports_1.5.0 ragg_1.5.0
[49] memoise_2.0.1 evaluate_1.0.5 rbibutils_2.3 miniUI_0.1.2
[53] profvis_0.4.0 rlang_1.1.6 Rcpp_1.1.0 xtable_1.8-4
[57] glue_1.8.0 pkgload_1.4.0 rstudioapi_0.17.1 teal.logger_0.4.0
[61] R6_2.6.1 systemfonts_1.2.3 fs_1.6.6
Relevant log output
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