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insightsengineering / teal

Exploratory Web Apps for Analyzing Clinical Trial Data
https://insightsengineering.github.io/teal/
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[Bug]: Duplicated library calls in SRC - devel deploy #1113

Closed pawelru closed 3 months ago

pawelru commented 6 months ago

What happened?

Some of the packages are displayed twice in the SRC. Tested devel deploy of exploratory app - Table Choices module - https://genentech.shinyapps.io/nest_exploratory_dev/

sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] sparkline_2.0                    colourpicker_1.3.0              
 [3] broom_1.0.5                      nestcolor_0.1.2.9009            
 [5] rtables_0.6.6.9011               magrittr_2.0.3                  
 [7] formatters_0.5.5.9010            rlang_1.1.3                     
 [9] MASS_7.3-60.0.1                  lattice_0.22-5                  
[11] jsonlite_1.8.8                   htmlwidgets_1.6.4               
[13] gridExtra_2.3                    goftest_1.2-3                   
[15] ggpmisc_0.5.5                    ggpp_0.5.6                      
[17] ggExtra_0.10.1                   tidyr_1.3.1                     
[19] dplyr_1.1.4                      scda.2022_0.1.5.9006            
[21] scda_0.1.6.9016                  teal.modules.general_0.2.16.9023
[23] teal.transform_0.5.0.9000        teal_0.15.1.9002                
[25] teal.slice_0.5.0.9003            teal.data_0.5.0.9001            
[27] teal.code_0.5.0.9003             shinyTree_0.3.1                 
[29] ggmosaic_0.3.3                   ggplot2_3.5.0                   
[31] shiny_1.8.0                     

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0         viridisLite_0.4.2        farver_2.1.1            
 [4] fastmap_1.1.1            lazyeval_0.2.2           promises_1.2.1          
 [7] shinyjs_2.1.0            digest_0.6.34            mime_0.12               
[10] lifecycle_1.0.4          ellipsis_0.3.2           survival_3.5-8          
[13] compiler_4.3.2           sass_0.4.8               tools_4.3.2             
[16] yaml_2.3.8               utf8_1.2.4               data.table_1.15.0       
[19] knitr_1.45               labeling_0.4.3           miniUI_0.1.1.1          
[22] withr_3.0.0              purrr_1.0.2              shinyWidgets_0.8.1      
[25] grid_4.3.2               fansi_1.0.6              teal.logger_0.1.3.9011  
[28] xtable_1.8-4             colorspace_2.1-0         scales_1.3.0            
[31] cli_3.6.2                rmarkdown_2.25           generics_0.1.3          
[34] httr_1.4.7               polynom_1.4-1            cachem_1.0.8            
[37] stringr_1.5.1            splines_4.3.2            vctrs_0.6.5             
[40] Matrix_1.6-5             SparseM_1.81             tern_0.9.3.9019         
[43] ggrepel_0.9.5            crosstalk_1.2.1          teal.widgets_0.4.2.9005 
[46] plotly_4.10.4            fontawesome_0.5.2        jquerylib_0.1.4         
[49] glue_1.7.0               DT_0.32                  stringi_1.8.3           
[52] gtable_0.3.4             later_1.3.2              shinycssloaders_1.0.0   
[55] munsell_0.5.0            tibble_3.2.1             logger_0.2.2            
[58] pillar_1.9.0             htmltools_0.5.7          quantreg_5.97           
[61] R6_2.5.1                 Rdpack_2.6               evaluate_0.23           
[64] rbibutils_2.2.16         backports_1.4.1          memoise_2.0.1           
[67] teal.reporter_0.3.0.9004 httpuv_1.6.14            bslib_0.6.1             
[70] MatrixModels_0.5-3       Rcpp_1.0.12              shinyvalidate_0.1.3     
[73] checkmate_2.3.1          xfun_0.42                forcats_1.0.0           
[76] pkgconfig_2.0.3         

### Relevant log output

```R
# Add any code to install/load your NEST environment here

library(shiny)
library(ggplot2)
library(ggmosaic)
library(shinyTree)
library(teal.code)
library(teal.data)
library(teal.slice)
library(teal)
library(teal.transform)
library(teal.modules.general)
library(scda)
library(scda.2022)
library(dplyr)
library(tidyr)
library(ggExtra)
library(ggpp)
library(ggpmisc)
library(goftest)
library(gridExtra)
library(htmlwidgets)
library(jsonlite)
library(lattice)
library(MASS)
library(rlang)
library(formatters)
library(magrittr)
library(rtables)
library(nestcolor)
library(broom)
library(colourpicker)
library(sparkline)

library(scda)
library(scda.2022)
library(dplyr)
library(tidyr)
library(ggExtra)
library(ggpmisc)
library(ggpp)
library(goftest)
library(gridExtra)
library(htmlwidgets)
library(jsonlite)
library(lattice)
library(MASS)
library(rlang)
library(rtables)
library(nestcolor)
library(broom)
library(colourpicker)
library(sparkline)
ADSL <- synthetic_cdisc_data("latest")$adsl

stopifnot(rlang::hash(ADSL) == "843e317c3d4aeb88062cd39a9c62fe8a")

ANL_1 <- ADSL %>% dplyr::select(STUDYID, USUBJID, STRATA2, ARMCD)
ANL <- ANL_1
ANL <- ANL %>% teal.data::col_relabel(STRATA2 = "Stratification Factor 2", ARMCD = "Planned Arm Code")
title <- "Cross-Table of Stratification Factor 2 [STRATA2] (rows) vs. Planned Arm Code [ARMCD] (columns)"
lyt <- rtables::basic_table() %>% rtables::split_cols_by("ARMCD", split_fun = rtables::add_overall_level(label = "Total", first = FALSE)) %>% rtables::add_colcounts() %>% tern::analyze_vars(vars = "STRATA2", var_labels = c(STRATA2 = "Stratification Factor 2 [STRATA2]"), na.rm = FALSE, denom = "N_col", .stats = c("mean_sd", "median", "range", "count_fraction"))
ANL <- tern::df_explicit_na(ANL)
tbl <- rtables::build_table(lyt = lyt, df = ANL[order(ANL[["ARMCD"]]), ])
tbl


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gogonzo commented 6 months ago

PR here https://github.com/insightsengineering/teal/pull/1015

gogonzo commented 3 months ago

Closing in favour of https://github.com/insightsengineering/teal/issues/1124