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[Bug]: qenv is valid but code is not reproducible

Aperta
  • Qualcosa non va?
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Valutazione

Difficoltà
4/5
Tempo stimato
3-5 giorni
Idoneità per principianti
38/100
Tipo di issue
Bug
Chiarezza
Abbastanza chiara
Stato di attività
Ferma
Stack tecnologico
r
Ambito
tooling

Direzione di ricerca

Riproduci gli esempi di within(qenv(), ...) in una sessione nuova di R --vanilla, quindi esamina l’inizializzazione di qenv e l’uso di .GlobalEnv. Confronta il comportamento quando teal.modules.clinical è caricato rispetto a quando è assente; il lavoro dovrebbe essere considerato completato impedendo che un qenv risulti valido quando il suo codice dipende da oggetti o funzioni non disponibili.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

bug core
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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