short fix

Signed-off-by: Awa Synthia <[email protected]>

NAMESPACE

@@ -99,6 +99,15 @@ export(wordcloud3)
 export(writeMSA_AA2FA)
 export(writeProcessRuntime2TSV)
 export(writeProcessRuntime2YML)
+import(DT)
+import(data.table)
+import(dplyr)
+import(httr)
+import(plotly)
+import(readr)
+import(rentrez)
+import(stringr)
+import(visNetwork)
 importFrom(Biostrings,AAStringSet)
 importFrom(Biostrings,readAAStringSet)
 importFrom(Biostrings,toString)

R/generate_report.R

@@ -1,7 +1,8 @@
 # Author(s): Awa Synthia
 # Last modified: 2024
 
-# load functions to use
+# import libs
+#' @import readr stringr
 
 #' @export
 # example usage: getCaseStudyReport("Acinetobacter baumannii", "Beta-lactams")

R/run_pipeline.R

@@ -1,8 +1,8 @@
 # Author(s): Awa Synthia
 # Last modified: 2024
 
-# Temporal fix. should work normally in descr
-library(readr)
+# import libs
+#' @import readr data.table httr rentrez
 
 getSeqs <- function(sequences,
                           acc_file_path = "accs.txt",

R/viz_utils.R

@@ -1,6 +1,9 @@
 # Author(s): Awa Synthia
 # Last modified: 2024
 
+# import libs
+#' @import dplyr stringr visNetwork DT plotly
+#'
 # Function to generate the InterProScan Visualization
 getIPRGenesVisualization <- function(data, app_data,
                                     query_iprDatabases = c("Pfam", "Phobius", "TMHMM", "Gene3D"),