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register teal.logger handlers #354

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merged 5 commits into from
Mar 20, 2024
Merged

register teal.logger handlers #354

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b73e48a
register teal.logger handlers
pawelru Feb 1, 2024
577ada4
Merge branch 'main' into register_handlers
pawelru Mar 11, 2024
4b4f035
Update DESCRIPTION
pawelru Mar 11, 2024
39d7cdb
Merge branch 'main' into register_handlers
donyunardi Mar 15, 2024
79e0df6
Update DESCRIPTION
pawelru Mar 20, 2024
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1 change: 0 additions & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@ repos:
- forcats
- bioc::hermes
- lifecycle
- logger
- bioc::MultiAssayExperiment
- rtables
- S4Vectors
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -40,7 +40,6 @@ Imports:
forcats,
hermes (>= 1.7.1),
lifecycle,
logger (>= 0.2.0),
MultiAssayExperiment,
rtables (>= 0.5.1),
S4Vectors,
Expand All @@ -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)
Expand All @@ -60,6 +59,7 @@ Suggests:
dplyr,
globals,
knitr,
logger (>= 0.2.0),
matrixStats,
R6,
rmarkdown,
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2 changes: 1 addition & 1 deletion R/barplot.R
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion R/boxplot.R
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion R/forestplot.R
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion R/km.R
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion R/pca.R
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion R/scatterplot.R
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion R/volcanoplot.R
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Expand Up @@ -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)
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1 change: 1 addition & 0 deletions R/zzz.R
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@@ -1,3 +1,4 @@
.onLoad <- function(libname, pkgname) { # nolint
teal.logger::register_logger(namespace = "teal.modules.hermes")
teal.logger::register_handlers("teal.modules.hermes")
}
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