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feat: allow passing of global settings launching from R or running docker container.

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Andreas Gammelgaard Damsbo 2026-03-11 13:22:54 +01:00
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5 changed files with 29 additions and 28 deletions
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2
NEWS.md
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@ -6,6 +6,8 @@
*NEW* New with_labels() function (and helpers) added to allow easy preservation of labels. *NEW* New with_labels() function (and helpers) added to allow easy preservation of labels.
*NEW* option to pass global settings when running as docker or launching from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT, DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Docs will follow.
# FreesearchR 26.3.1 # FreesearchR 26.3.1
*FIX* ~~Include font files for static loading without dependency on Google.~~ Kept webfonts from google as local fonts are not working for now. *FIX* ~~Include font files for static loading without dependency on Google.~~ Kept webfonts from google as local fonts are not working for now.

28
R/launch_FreesearchR.R
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@ -23,11 +23,11 @@ launch_FreesearchR <- function(inlcude_globalenv = TRUE,
data_limit_upper = 100000, data_limit_upper = 100000,
data_limit_lower = 1, data_limit_lower = 1,
...) { ...) {
global_freesearchR <- list( Sys.setenv(
include_globalenv = include_globalenv, INCLUDE_GLOBALENV = include_globalenv,
data_limit_default = data_limit_default, DATA_LIMIT_DEFAULT = data_limit_default,
data_limit_upper = data_limit_upper, DATA_LIMIT_UPPER = data_limit_upper,
data_limit_lower = data_limit_lower DATA_LIMIT_LOWER = data_limit_lower
) )
appDir <- system.file("apps", "FreesearchR", package = "FreesearchR") appDir <- system.file("apps", "FreesearchR", package = "FreesearchR")
@ -39,3 +39,21 @@ launch_FreesearchR <- function(inlcude_globalenv = TRUE,
a <- shiny::runApp(appDir = paste0(appDir, "/app.R"), ...) a <- shiny::runApp(appDir = paste0(appDir, "/app.R"), ...)
return(invisible(a)) return(invisible(a))
} }
## Helper to set env variables
get_config <- function(var_name, default = NULL) {
# First check environment variables (set by Docker)
val <- Sys.getenv(var_name, unset = NA)
if (!is.na(val) && nzchar(val)) {
return(val)
}
# Fall back to default (can be overridden when launching from R)
if (!is.null(default)) {
return(default)
}
stop(paste("Required config variable not set:", var_name))
}

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R/sysdata.rda
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8
R/ui_elements.R
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@ -83,9 +83,9 @@ ui_elements <- function(selection) {
layout_params = "dropdown", layout_params = "dropdown",
# title = "Choose a datafile to upload", # title = "Choose a datafile to upload",
file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".ods", ".dta"), file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".ods", ".dta"),
limit_default = global_freesearchR$data_limit_default, limit_default = DATA_LIMIT_DEFAULT,
limit_lower = global_freesearchR$data_limit_lower, limit_lower = DATA_LIMIT_LOWER,
limit_upper = global_freesearchR$data_limit_upper limit_upper = DATA_LIMIT_UPPER
) )
), ),
@ -107,7 +107,7 @@ ui_elements <- function(selection) {
id = "env", id = "env",
title = NULL, title = NULL,
packages = c("NHANES", "stRoke", "datasets", "MASS"), packages = c("NHANES", "stRoke", "datasets", "MASS"),
globalenv = global_freesearchR$include_globalenv globalenv = isTruthy(INCLUDE_GLOBALENV)
) )
), ),
# shiny::conditionalPanel( # shiny::conditionalPanel(

19
SESSION.md
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@ -26,8 +26,6 @@
|apexcharter |0.4.5 |2026-01-07 |CRAN (R 4.5.2) | |apexcharter |0.4.5 |2026-01-07 |CRAN (R 4.5.2) |
|askpass |1.2.1 |2024-10-04 |CRAN (R 4.5.0) | |askpass |1.2.1 |2024-10-04 |CRAN (R 4.5.0) |
|assertthat |0.2.1 |2019-03-21 |CRAN (R 4.5.0) | |assertthat |0.2.1 |2019-03-21 |CRAN (R 4.5.0) |
|attachment |0.4.5 |2025-03-14 |CRAN (R 4.5.0) |
|attempt |0.3.1 |2020-05-03 |CRAN (R 4.5.0) |
|backports |1.5.0 |2024-05-23 |CRAN (R 4.5.0) | |backports |1.5.0 |2024-05-23 |CRAN (R 4.5.0) |
|base64enc |0.1-6 |2026-02-02 |CRAN (R 4.5.2) | |base64enc |0.1-6 |2026-02-02 |CRAN (R 4.5.2) |
|bayestestR |0.17.0 |2025-08-29 |CRAN (R 4.5.0) | |bayestestR |0.17.0 |2025-08-29 |CRAN (R 4.5.0) |
@ -46,7 +44,6 @@
|cardx |0.3.2 |2026-02-05 |CRAN (R 4.5.2) | |cardx |0.3.2 |2026-02-05 |CRAN (R 4.5.2) |
|caTools |1.18.3 |2024-09-04 |CRAN (R 4.5.0) | |caTools |1.18.3 |2024-09-04 |CRAN (R 4.5.0) |
|cellranger |1.1.0 |2016-07-27 |CRAN (R 4.5.0) | |cellranger |1.1.0 |2016-07-27 |CRAN (R 4.5.0) |
|cffr |1.2.1 |2026-01-12 |CRAN (R 4.5.2) |
|checkmate |2.3.4 |2026-02-03 |CRAN (R 4.5.2) | |checkmate |2.3.4 |2026-02-03 |CRAN (R 4.5.2) |
|class |7.3-23 |2025-01-01 |CRAN (R 4.5.2) | |class |7.3-23 |2025-01-01 |CRAN (R 4.5.2) |
|classInt |0.4-11 |2025-01-08 |CRAN (R 4.5.0) | |classInt |0.4-11 |2025-01-08 |CRAN (R 4.5.0) |
@ -56,8 +53,6 @@
|colorspace |2.1-2 |2025-09-22 |CRAN (R 4.5.0) | |colorspace |2.1-2 |2025-09-22 |CRAN (R 4.5.0) |
|commonmark |2.0.0 |2025-07-07 |CRAN (R 4.5.0) | |commonmark |2.0.0 |2025-07-07 |CRAN (R 4.5.0) |
|crayon |1.5.3 |2024-06-20 |CRAN (R 4.5.0) | |crayon |1.5.3 |2024-06-20 |CRAN (R 4.5.0) |
|credentials |2.0.3 |2025-09-12 |CRAN (R 4.5.0) |
|curl |7.0.0 |2025-08-19 |CRAN (R 4.5.0) |
|data.table |1.18.2.1 |2026-01-27 |CRAN (R 4.5.2) | |data.table |1.18.2.1 |2026-01-27 |CRAN (R 4.5.2) |
|datamods |1.5.3 |2024-10-02 |CRAN (R 4.5.0) | |datamods |1.5.3 |2024-10-02 |CRAN (R 4.5.0) |
|datawizard |1.3.0 |2025-10-11 |CRAN (R 4.5.0) | |datawizard |1.3.0 |2025-10-11 |CRAN (R 4.5.0) |
@ -66,7 +61,6 @@
|devtools |2.4.6 |2025-10-03 |CRAN (R 4.5.0) | |devtools |2.4.6 |2025-10-03 |CRAN (R 4.5.0) |
|DHARMa |0.4.7 |2024-10-18 |CRAN (R 4.5.0) | |DHARMa |0.4.7 |2024-10-18 |CRAN (R 4.5.0) |
|digest |0.6.39 |2025-11-19 |CRAN (R 4.5.2) | |digest |0.6.39 |2025-11-19 |CRAN (R 4.5.2) |
|dockerfiler |0.2.5 |2025-05-07 |CRAN (R 4.5.0) |
|doParallel |1.0.17 |2022-02-07 |CRAN (R 4.5.0) | |doParallel |1.0.17 |2022-02-07 |CRAN (R 4.5.0) |
|dplyr |1.2.0 |2026-02-03 |CRAN (R 4.5.2) | |dplyr |1.2.0 |2026-02-03 |CRAN (R 4.5.2) |
|DT |0.34.0 |2025-09-02 |CRAN (R 4.5.0) | |DT |0.34.0 |2025-09-02 |CRAN (R 4.5.0) |
@ -93,15 +87,12 @@
|fs |1.6.6 |2025-04-12 |CRAN (R 4.5.0) | |fs |1.6.6 |2025-04-12 |CRAN (R 4.5.0) |
|gdtools |0.5.0 |2026-02-09 |CRAN (R 4.5.2) | |gdtools |0.5.0 |2026-02-09 |CRAN (R 4.5.2) |
|generics |0.1.4 |2025-05-09 |CRAN (R 4.5.0) | |generics |0.1.4 |2025-05-09 |CRAN (R 4.5.0) |
|gert |2.3.1 |2026-01-11 |CRAN (R 4.5.2) |
|ggalluvial |0.12.5 |2023-02-22 |CRAN (R 4.5.0) | |ggalluvial |0.12.5 |2023-02-22 |CRAN (R 4.5.0) |
|ggcorrplot |0.1.4.1 |2023-09-05 |CRAN (R 4.5.0) | |ggcorrplot |0.1.4.1 |2023-09-05 |CRAN (R 4.5.0) |
|ggforce |0.5.0 |2025-06-18 |CRAN (R 4.5.0) | |ggforce |0.5.0 |2025-06-18 |CRAN (R 4.5.0) |
|ggplot2 |4.0.2 |2026-02-03 |CRAN (R 4.5.2) | |ggplot2 |4.0.2 |2026-02-03 |CRAN (R 4.5.2) |
|ggridges |0.5.7 |2025-08-27 |CRAN (R 4.5.0) | |ggridges |0.5.7 |2025-08-27 |CRAN (R 4.5.0) |
|ggstats |0.12.0 |2025-12-22 |CRAN (R 4.5.2) | |ggstats |0.12.0 |2025-12-22 |CRAN (R 4.5.2) |
|gh |1.5.0 |2025-05-26 |CRAN (R 4.5.0) |
|gitcreds |0.1.2 |2022-09-08 |CRAN (R 4.5.0) |
|glue |1.8.0 |2024-09-30 |CRAN (R 4.5.0) | |glue |1.8.0 |2024-09-30 |CRAN (R 4.5.0) |
|gridExtra |2.3 |2017-09-09 |CRAN (R 4.5.0) | |gridExtra |2.3 |2017-09-09 |CRAN (R 4.5.0) |
|gt |1.3.0 |2026-01-22 |CRAN (R 4.5.2) | |gt |1.3.0 |2026-01-22 |CRAN (R 4.5.2) |
@ -115,24 +106,20 @@
|htmltools |0.5.9 |2025-12-04 |CRAN (R 4.5.2) | |htmltools |0.5.9 |2025-12-04 |CRAN (R 4.5.2) |
|htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.5.0) | |htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.5.0) |
|httpuv |1.6.16 |2025-04-16 |CRAN (R 4.5.0) | |httpuv |1.6.16 |2025-04-16 |CRAN (R 4.5.0) |
|httr2 |1.2.2 |2025-12-08 |CRAN (R 4.5.2) |
|IDEAFilter |0.2.1 |2025-07-29 |CRAN (R 4.5.0) | |IDEAFilter |0.2.1 |2025-07-29 |CRAN (R 4.5.0) |
|insight |1.4.6 |2026-02-04 |CRAN (R 4.5.2) | |insight |1.4.6 |2026-02-04 |CRAN (R 4.5.2) |
|iterators |1.0.14 |2022-02-05 |CRAN (R 4.5.0) | |iterators |1.0.14 |2022-02-05 |CRAN (R 4.5.0) |
|jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.5.0) | |jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.5.0) |
|jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.5.0) | |jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.5.0) |
|jsonvalidate |1.5.0 |2025-02-07 |CRAN (R 4.5.0) |
|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.5.2) | |KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.5.2) |
|keyring |1.4.1 |2025-06-15 |CRAN (R 4.5.0) | |keyring |1.4.1 |2025-06-15 |CRAN (R 4.5.0) |
|knitr |1.51 |2025-12-20 |CRAN (R 4.5.2) | |knitr |1.51 |2025-12-20 |CRAN (R 4.5.2) |
|later |1.4.6 |2026-02-13 |CRAN (R 4.5.2) | |later |1.4.6 |2026-02-13 |CRAN (R 4.5.2) |
|lattice |0.22-7 |2025-04-02 |CRAN (R 4.5.2) | |lattice |0.22-7 |2025-04-02 |CRAN (R 4.5.2) |
|lifecycle |1.0.5 |2026-01-08 |CRAN (R 4.5.2) | |lifecycle |1.0.5 |2026-01-08 |CRAN (R 4.5.2) |
|litedown |0.9 |2025-12-18 |CRAN (R 4.5.2) |
|lme4 |1.1-38 |2025-12-02 |CRAN (R 4.5.2) | |lme4 |1.1-38 |2025-12-02 |CRAN (R 4.5.2) |
|lubridate |1.9.5 |2026-02-04 |CRAN (R 4.5.2) | |lubridate |1.9.5 |2026-02-04 |CRAN (R 4.5.2) |
|magrittr |2.0.4 |2025-09-12 |CRAN (R 4.5.0) | |magrittr |2.0.4 |2025-09-12 |CRAN (R 4.5.0) |
|markdown |2.0 |2025-03-23 |CRAN (R 4.5.0) |
|MASS |7.3-65 |2025-02-28 |CRAN (R 4.5.0) | |MASS |7.3-65 |2025-02-28 |CRAN (R 4.5.0) |
|Matrix |1.7-4 |2025-08-28 |CRAN (R 4.5.2) | |Matrix |1.7-4 |2025-08-28 |CRAN (R 4.5.2) |
|memoise |2.0.1 |2021-11-26 |CRAN (R 4.5.0) | |memoise |2.0.1 |2021-11-26 |CRAN (R 4.5.0) |
@ -148,7 +135,6 @@
|openssl |2.3.4 |2025-09-30 |CRAN (R 4.5.0) | |openssl |2.3.4 |2025-09-30 |CRAN (R 4.5.0) |
|openxlsx2 |1.23.1 |2026-01-19 |CRAN (R 4.5.2) | |openxlsx2 |1.23.1 |2026-01-19 |CRAN (R 4.5.2) |
|otel |0.2.0 |2025-08-29 |CRAN (R 4.5.0) | |otel |0.2.0 |2025-08-29 |CRAN (R 4.5.0) |
|pak |0.9.2 |2025-12-22 |CRAN (R 4.5.2) |
|parameters |0.28.3 |2025-11-25 |CRAN (R 4.5.2) | |parameters |0.28.3 |2025-11-25 |CRAN (R 4.5.2) |
|patchwork |1.3.2 |2025-08-25 |CRAN (R 4.5.0) | |patchwork |1.3.2 |2025-08-25 |CRAN (R 4.5.0) |
|pbmcapply |1.5.1 |2022-04-28 |CRAN (R 4.5.0) | |pbmcapply |1.5.1 |2022-04-28 |CRAN (R 4.5.0) |
@ -172,7 +158,6 @@
|R6 |2.6.1 |2025-02-15 |CRAN (R 4.5.0) | |R6 |2.6.1 |2025-02-15 |CRAN (R 4.5.0) |
|ragg |1.5.0 |2025-09-02 |CRAN (R 4.5.0) | |ragg |1.5.0 |2025-09-02 |CRAN (R 4.5.0) |
|rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.5.0) | |rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.5.0) |
|rappdirs |0.3.4 |2026-01-17 |CRAN (R 4.5.2) |
|rbibutils |2.4.1 |2026-01-21 |CRAN (R 4.5.2) | |rbibutils |2.4.1 |2026-01-21 |CRAN (R 4.5.2) |
|RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.5.0) | |RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.5.0) |
|Rcpp |1.1.1 |2026-01-10 |CRAN (R 4.5.2) | |Rcpp |1.1.1 |2026-01-10 |CRAN (R 4.5.2) |
@ -205,7 +190,6 @@
|sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.5.0) | |sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.5.0) |
|shiny |1.13.0 |2026-02-20 |CRAN (R 4.5.2) | |shiny |1.13.0 |2026-02-20 |CRAN (R 4.5.2) |
|shiny.i18n |0.3.0 |2023-01-16 |CRAN (R 4.5.0) | |shiny.i18n |0.3.0 |2023-01-16 |CRAN (R 4.5.0) |
|shiny2docker |0.0.3 |2025-06-28 |CRAN (R 4.5.0) |
|shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.5.0) | |shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.5.0) |
|shinyjs |2.1.1 |2026-01-15 |CRAN (R 4.5.2) | |shinyjs |2.1.1 |2026-01-15 |CRAN (R 4.5.2) |
|shinyTime |1.0.3 |2022-08-19 |CRAN (R 4.5.0) | |shinyTime |1.0.3 |2022-08-19 |CRAN (R 4.5.0) |
@ -214,7 +198,6 @@
|stringi |1.8.7 |2025-03-27 |CRAN (R 4.5.0) | |stringi |1.8.7 |2025-03-27 |CRAN (R 4.5.0) |
|stringr |1.6.0 |2025-11-04 |CRAN (R 4.5.0) | |stringr |1.6.0 |2025-11-04 |CRAN (R 4.5.0) |
|stRoke |25.9.2 |2025-09-30 |CRAN (R 4.5.0) | |stRoke |25.9.2 |2025-09-30 |CRAN (R 4.5.0) |
|sys |3.4.3 |2024-10-04 |CRAN (R 4.5.0) |
|systemfonts |1.3.1 |2025-10-01 |CRAN (R 4.5.0) | |systemfonts |1.3.1 |2025-10-01 |CRAN (R 4.5.0) |
|testthat |3.3.2 |2026-01-11 |CRAN (R 4.5.2) | |testthat |3.3.2 |2026-01-11 |CRAN (R 4.5.2) |
|textshaping |1.0.4 |2025-10-10 |CRAN (R 4.5.0) | |textshaping |1.0.4 |2025-10-10 |CRAN (R 4.5.0) |
@ -229,7 +212,6 @@
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|uuid |1.2-2 |2026-01-23 |CRAN (R 4.5.2) | |uuid |1.2-2 |2026-01-23 |CRAN (R 4.5.2) |
|V8 |8.0.1 |2025-10-10 |CRAN (R 4.5.0) |
|vctrs |0.7.1 |2026-01-23 |CRAN (R 4.5.2) | |vctrs |0.7.1 |2026-01-23 |CRAN (R 4.5.2) |
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@ -240,5 +222,4 @@
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|xtable |1.8-4 |2019-04-21 |CRAN (R 4.5.0) | |xtable |1.8-4 |2019-04-21 |CRAN (R 4.5.0) |
|yaml |2.3.12 |2025-12-10 |CRAN (R 4.5.2) | |yaml |2.3.12 |2025-12-10 |CRAN (R 4.5.2) |
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|zip |2.3.3 |2025-05-13 |CRAN (R 4.5.0) | |zip |2.3.3 |2025-05-13 |CRAN (R 4.5.0) |