register teal.logger handlers

.pre-commit-config.yaml

@@ -25,7 +25,6 @@ repos:
           - DT
           - forcats
           - grid
-          - logger
           - magrittr
           - scales
           - shinyjs

DESCRIPTION

@@ -29,7 +29,6 @@ Imports:
     DT (>= 0.13),
     forcats (>= 1.0.0),
     grid,
-    logger (>= 0.2.0),
     magrittr (>= 1.5),
     scales,
     shinyjs,
@@ -38,7 +37,7 @@ Imports:
     stats,
     stringr (>= 1.4.1),
     teal.code (>= 0.4.1.9009),
-    teal.logger (>= 0.1.1),
+    teal.logger (>= 0.1.3.9010),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0),
     tern (>= 0.7.10),
@@ -58,6 +57,7 @@ Suggests:
     jsonlite,
     knitr (>= 1.42),
     lattice (>= 0.18-4),
+    logger (>= 0.2.0),
     MASS,
     methods,
     nestcolor (>= 0.1.0),
@@ -71,15 +71,15 @@ VignetteBuilder:
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     rstudio/shiny, shinyTree/shinyTree, insightsengineering/teal,
     mllg/checkmate, tidyverse/dplyr, rstudio/DT, tidyverse/forcats,
-    daroczig/logger, tidyverse/magrittr, r-lib/scales, daattali/shinyjs,
+    tidyverse/magrittr, r-lib/scales, daattali/shinyjs,
     rstudio/shinyvalidate, dreamRs/shinyWidgets, tidyverse/stringr,
     insightsengineering/teal.code, insightsengineering/teal.logger,
     insightsengineering/teal.reporter, insightsengineering/teal.transform,
     insightsengineering/teal.widgets, insightsengineering/tern,
     tidyverse/tibble, tidyverse/tidyr, r-lib/tidyselect, tidymodels/broom,
     daattali/colourpicker, daattali/ggExtra, aphalo/ggpmisc, aphalo/ggpp,
     baddstats/goftest, gridExtra, ramnathv/htmlwidgets, jeroen/jsonlite,
-    yihui/knitr, deepayan/lattice, MASS, insightsengineering/nestcolor,
+    yihui/knitr, deepayan/lattice, daroczig/logger, MASS, insightsengineering/nestcolor,
     r-lib/rlang, insightsengineering/rtables, sparkline,
     insightsengineering/teal.data, r-lib/testthat
 Config/Needs/website: insightsengineering/nesttemplate

R/tm_a_pca.R

@@ -69,7 +69,7 @@ tm_a_pca <- function(label = "Principal Component Analysis",
                      size = c(2, 1, 8),
                      pre_output = NULL,
                      post_output = NULL) {
-  logger::log_info("Initializing tm_a_pca")
+  message("Initializing tm_a_pca")
   if (inherits(dat, "data_extract_spec")) dat <- list(dat)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 

R/tm_a_regression.R

@@ -93,7 +93,7 @@ tm_a_regression <- function(label = "Regression Analysis",
                             post_output = NULL,
                             default_plot_type = 1,
                             default_outlier_label = "USUBJID") {
-  logger::log_info("Initializing tm_a_regression")
+  message("Initializing tm_a_regression")
   if (inherits(regressor, "data_extract_spec")) regressor <- list(regressor)
   if (inherits(response, "data_extract_spec")) response <- list(response)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)

R/tm_data_table.R

@@ -62,7 +62,7 @@ tm_data_table <- function(label = "Data Table",
                           server_rendering = FALSE,
                           pre_output = NULL,
                           post_output = NULL) {
-  logger::log_info("Initializing tm_data_table")
+  message("Initializing tm_data_table")
   checkmate::assert_string(label)
   checkmate::assert_list(variables_selected, min.len = 0, types = "character", names = "named")
   if (length(variables_selected) > 0) {

R/tm_file_viewer.R

@@ -39,7 +39,7 @@
 #'
 tm_file_viewer <- function(label = "File Viewer Module",
                            input_path = list("Current Working Directory" = ".")) {
-  logger::log_info("Initializing tm_file_viewer")
+  message("Initializing tm_file_viewer")
   if (length(label) == 0 || identical(label, "")) {
     label <- " "
   }

R/tm_front_page.R

@@ -70,7 +70,7 @@ tm_front_page <- function(label = "Front page",
   checkmate::assert_character(footnotes, min.len = 0, any.missing = FALSE)
   checkmate::assert_flag(show_metadata)
 
-  logger::log_info("Initializing tm_front_page")
+  message("Initializing tm_front_page")
   args <- as.list(environment())
 
   module(

R/tm_g_association.R

@@ -89,7 +89,7 @@ tm_g_association <- function(label = "Association",
                              pre_output = NULL,
                              post_output = NULL,
                              ggplot2_args = teal.widgets::ggplot2_args()) {
-  logger::log_info("Initializing tm_g_association")
+  message("Initializing tm_g_association")
   if (inherits(ref, "data_extract_spec")) ref <- list(ref)
   if (inherits(vars, "data_extract_spec")) vars <- list(vars)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)

R/tm_g_bivariate.R

@@ -125,7 +125,7 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
                            ggplot2_args = teal.widgets::ggplot2_args(),
                            pre_output = NULL,
                            post_output = NULL) {
-  logger::log_info("Initializing tm_g_bivariate")
+  message("Initializing tm_g_bivariate")
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(y, "data_extract_spec")) y <- list(y)
   if (inherits(row_facet, "data_extract_spec")) row_facet <- list(row_facet)

R/tm_g_distribution.R

@@ -119,7 +119,7 @@ tm_g_distribution <- function(label = "Distribution Module",
                               plot_width = NULL,
                               pre_output = NULL,
                               post_output = NULL) {
-  logger::log_info("Initializing tm_g_distribution")
+  message("Initializing tm_g_distribution")
 
   extra_packages <- c("ggpmisc", "ggpp", "goftest", "MASS", "broom")
   missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)

R/tm_g_response.R

@@ -85,7 +85,7 @@ tm_g_response <- function(label = "Response Plot",
                           ggplot2_args = teal.widgets::ggplot2_args(),
                           pre_output = NULL,
                           post_output = NULL) {
-  logger::log_info("Initializing tm_g_response")
+  message("Initializing tm_g_response")
   if (inherits(response, "data_extract_spec")) response <- list(response)
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(row_facet, "data_extract_spec")) row_facet <- list(row_facet)

R/tm_g_scatterplot.R

@@ -160,7 +160,7 @@ tm_g_scatterplot <- function(label = "Scatterplot",
                              post_output = NULL,
                              table_dec = 4,
                              ggplot2_args = teal.widgets::ggplot2_args()) {
-  logger::log_info("Initializing tm_g_scatterplot")
+  message("Initializing tm_g_scatterplot")
 
   extra_packages <- c("ggpmisc", "ggExtra", "colourpicker")
   missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)

R/tm_g_scatterplotmatrix.R

@@ -77,7 +77,7 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
                                    plot_width = NULL,
                                    pre_output = NULL,
                                    post_output = NULL) {
-  logger::log_info("Initializing tm_g_scatterplotmatrix")
+  message("Initializing tm_g_scatterplotmatrix")
   if (!requireNamespace("lattice", quietly = TRUE)) {
     stop("Cannot load lattice - please install the package or restart your session.")
   }

R/tm_missing_data.R

@@ -64,7 +64,7 @@ tm_missing_data <- function(label = "Missing data",
   if (!requireNamespace("rlang", quietly = TRUE)) {
     stop("Cannot load rlang - please install the package or restart your session.")
   }
-  logger::log_info("Initializing tm_missing_data")
+  message("Initializing tm_missing_data")
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
   checkmate::assert_string(label)

R/tm_outliers.R

@@ -75,7 +75,7 @@ tm_outliers <- function(label = "Outliers Module",
                         plot_width = NULL,
                         pre_output = NULL,
                         post_output = NULL) {
-  logger::log_info("Initializing tm_outliers")
+  message("Initializing tm_outliers")
   if (inherits(outlier_var, "data_extract_spec")) outlier_var <- list(outlier_var)
   if (inherits(categorical_var, "data_extract_spec")) categorical_var <- list(categorical_var)
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)

R/tm_t_crosstable.R

@@ -80,7 +80,7 @@ tm_t_crosstable <- function(label = "Cross Table",
                             pre_output = NULL,
                             post_output = NULL,
                             basic_table_args = teal.widgets::basic_table_args()) {
-  logger::log_info("Initializing tm_t_crosstable")
+  message("Initializing tm_t_crosstable")
   if (!requireNamespace("rtables", quietly = TRUE)) {
     stop("Cannot load rtables - please install the package or restart your session.")
   }

R/tm_variable_browser.R

@@ -62,7 +62,7 @@ tm_variable_browser <- function(label = "Variable Browser",
                                 pre_output = NULL,
                                 post_output = NULL,
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
-  logger::log_info("Initializing tm_variable_browser")
+  message("Initializing tm_variable_browser")
   if (!requireNamespace("sparkline", quietly = TRUE)) {
     stop("Cannot load sparkline - please install the package or restart your session.")
   }

R/zzz.R

@@ -1,3 +1,4 @@
 .onLoad <- function(libname, pkgname) { # nolint
   teal.logger::register_logger(namespace = "teal.modules.general")
+  teal.logger::register_handlers("teal.modules.general")
 }

tests/testthat/setup-logger.R

@@ -0,0 +1 @@
+logger::log_appender(function(...) NULL, namespace = "teal.modules.general")