From 3336364f2c658a7d243b69fd7263ebca59615c4c Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Wed, 20 Mar 2024 15:29:39 +0100
Subject: [PATCH] register teal.logger handlers (#354)

close https://github.com/insightsengineering/coredev-tasks/issues/502
test with https://github.com/insightsengineering/teal.logger/pull/73

As a bonus, we can safely move `logger` to suggests (it's still used in
tests)

---------

Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Co-authored-by: Dony Unardi <donyunardi@gmail.com>
---
 .pre-commit-config.yaml | 1 -
 DESCRIPTION             | 4 ++--
 R/barplot.R             | 2 +-
 R/boxplot.R             | 2 +-
 R/forestplot.R          | 2 +-
 R/km.R                  | 2 +-
 R/pca.R                 | 2 +-
 R/scatterplot.R         | 2 +-
 R/volcanoplot.R         | 2 +-
 R/zzz.R                 | 1 +
 10 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c34dab47..84f0a320 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -24,7 +24,6 @@ repos:
           - forcats
           - bioc::hermes
           - lifecycle
-          - logger
           - bioc::MultiAssayExperiment
           - rtables
           - S4Vectors
diff --git a/DESCRIPTION b/DESCRIPTION
index 62cf8386..a2d9141c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -40,7 +40,6 @@ Imports:
     forcats,
     hermes (>= 1.7.1),
     lifecycle,
-    logger (>= 0.2.0),
     MultiAssayExperiment,
     rtables (>= 0.5.1),
     S4Vectors,
@@ -50,7 +49,7 @@ Imports:
     stringr,
     SummarizedExperiment,
     teal.data (>= 0.3.0.9018),
-    teal.logger (>= 0.1.1),
+    teal.logger (>= 0.1.3.9013),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0),
     tern (>= 0.7.10)
@@ -60,6 +59,7 @@ Suggests:
     dplyr,
     globals,
     knitr,
+    logger (>= 0.2.0),
     matrixStats,
     R6,
     rmarkdown,
diff --git a/R/barplot.R b/R/barplot.R
index a221827e..11b5deb9 100644
--- a/R/barplot.R
+++ b/R/barplot.R
@@ -35,7 +35,7 @@ tm_g_barplot <- function(label,
                          ),
                          pre_output = NULL,
                          post_output = NULL) {
-  logger::log_info("Initializing tm_g_barplot")
+  message("Initializing tm_g_barplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays)
diff --git a/R/boxplot.R b/R/boxplot.R
index bdccb1db..7eccbb6f 100644
--- a/R/boxplot.R
+++ b/R/boxplot.R
@@ -36,7 +36,7 @@ tm_g_boxplot <- function(label,
                          ),
                          pre_output = NULL,
                          post_output = NULL) {
-  logger::log_info("Initializing tm_g_boxplot")
+  message("Initializing tm_g_boxplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays, any.missing = FALSE)
diff --git a/R/forestplot.R b/R/forestplot.R
index 36ce927b..8374e4da 100644
--- a/R/forestplot.R
+++ b/R/forestplot.R
@@ -54,7 +54,7 @@ tm_g_forest_tte <- function(label,
                             post_output = NULL,
                             plot_height = c(600L, 200L, 2000L),
                             plot_width = c(1360L, 500L, 2000L)) {
-  logger::log_info("Initializing tm_g_forest_tte")
+  message("Initializing tm_g_forest_tte")
   assert_string(label)
   assert_string(adtte_name)
   assert_string(mae_name)
diff --git a/R/km.R b/R/km.R
index 9f72906e..b2ff88f6 100644
--- a/R/km.R
+++ b/R/km.R
@@ -57,7 +57,7 @@ tm_g_km <- function(label,
                     ),
                     pre_output = NULL,
                     post_output = NULL) {
-  logger::log_info("Initializing tm_g_km")
+  message("Initializing tm_g_km")
   assert_string(label)
   assert_string(adtte_name)
   assert_string(mae_name)
diff --git a/R/pca.R b/R/pca.R
index 1e1871e5..a873a29e 100644
--- a/R/pca.R
+++ b/R/pca.R
@@ -30,7 +30,7 @@ tm_g_pca <- function(label,
                      exclude_assays = character(),
                      pre_output = NULL,
                      post_output = NULL) {
-  logger::log_info("Initializing tm_g_pca")
+  message("Initializing tm_g_pca")
   assert_string(label)
   assert_string(mae_name)
   assert_tag(pre_output, null.ok = TRUE)
diff --git a/R/scatterplot.R b/R/scatterplot.R
index 2004144c..6a09a89e 100644
--- a/R/scatterplot.R
+++ b/R/scatterplot.R
@@ -35,7 +35,7 @@ tm_g_scatterplot <- function(label,
                              ),
                              pre_output = NULL,
                              post_output = NULL) {
-  logger::log_info("Initializing tm_g_scatterplot")
+  message("Initializing tm_g_scatterplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays, any.missing = FALSE)
diff --git a/R/volcanoplot.R b/R/volcanoplot.R
index 217ac1a0..a15989ba 100644
--- a/R/volcanoplot.R
+++ b/R/volcanoplot.R
@@ -30,7 +30,7 @@ tm_g_volcanoplot <- function(label,
                              exclude_assays = character(),
                              pre_output = NULL,
                              post_output = NULL) {
-  logger::log_info("Initializing tm_g_volcanoplot")
+  message("Initializing tm_g_volcanoplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays)
diff --git a/R/zzz.R b/R/zzz.R
index 3009dba0..c317d6c9 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,3 +1,4 @@
 .onLoad <- function(libname, pkgname) { # nolint
   teal.logger::register_logger(namespace = "teal.modules.hermes")
+  teal.logger::register_handlers("teal.modules.hermes")
 }