diff --git a/NAMESPACE b/NAMESPACE
index 6ae464f6..3a7b5c03 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -247,6 +247,7 @@ importFrom(shiny,showNotification)
 importFrom(stats,as.formula)
 importFrom(stats,complete.cases)
 importFrom(stats,logLik)
+importFrom(stats,median)
 importFrom(stats,na.omit)
 importFrom(stringi,stri_extract_all_regex)
 importFrom(stringi,stri_replace_all_regex)
@@ -276,6 +277,7 @@ importFrom(tidyr,replace_na)
 importFrom(tidyr,separate)
 importFrom(tidyr,unite)
 importFrom(utils,combn)
+importFrom(utils,globalVariables)
 importFrom(viridis,scale_fill_viridis)
 importFrom(visNetwork,visEdges)
 importFrom(visNetwork,visGroups)
diff --git a/R/assign_job_queue.R b/R/assign_job_queue.R
index e481f400..9d9b6590 100644
--- a/R/assign_job_queue.R
+++ b/R/assign_job_queue.R
@@ -92,7 +92,8 @@ mapAdvOption2Process <- function(advanced_opts) {
 #'
 #' @importFrom dplyr across everything select summarise
 #' @importFrom rlang warn abort inform
-#'
+#' @importFrom stats median
+#' 
 #' @return [list] names: processes; values: median runtime (seconds)
 #'
 #' see molevol_scripts/R/metrics.R for info on functions called here
@@ -210,7 +211,7 @@ writeProcessRuntime2TSV <- function(dir_job_results, filepath) {
         names_to = "process",
         values_to = "median_seconds"
       ) |>
-      dplyr::arrange(dplyr::desc(median_seconds))
+      dplyr::arrange(dplyr::desc(.data$median_seconds))
 
     # Write the resulting tibble to a TSV file
     readr::write_tsv(df_proc_medians, file = filepath)
diff --git a/R/globals.R b/R/globals.R
new file mode 100644
index 00000000..76da9d5d
--- /dev/null
+++ b/R/globals.R
@@ -0,0 +1,4 @@
+# File to put all data.table variables that aren't defined otherwise
+
+#' @importFrom utils globalVariables
+utils::globalVariables(c("Protein"))
\ No newline at end of file
diff --git a/R/lineage.R b/R/lineage.R
index 46249c91..fa113654 100644
--- a/R/lineage.R
+++ b/R/lineage.R
@@ -432,7 +432,7 @@ IPG2Lineage <- function(accessions, ipg_file,
 
 
     lins <- GCA2Lineage(prot_data = ipg_dt, assembly_path, lineagelookup_path)
-    lins <- lins[!is.na(Lineage)] %>% unique()
+    lins <- lins[!is.na(.data$Lineage)] %>% unique()
 
     return(lins)
 }
diff --git a/R/msa.R b/R/msa.R
index 8838fdda..f0ee4b07 100644
--- a/R/msa.R
+++ b/R/msa.R
@@ -196,7 +196,7 @@ createMSA_PDF <- function(fasta_path, out_path = NULL,
 #' will be saved.
 #'
 #' @importFrom Biostrings readAAStringSet
-#'
+#' 
 #' @return A list containing the alignment object and the output file path.
 #' @export
 #'
diff --git a/R/tree.R b/R/tree.R
index ddbf9d61..5679de34 100755
--- a/R/tree.R
+++ b/R/tree.R
@@ -59,9 +59,6 @@
 convertFA2Tree <- function(fa_path = here("data/alns/pspa_snf7.fa"),
     tre_path = here("data/alns/pspa_snf7.tre"),
     fasttree_path = here("src/FastTree")) {
-    # fa_path=here("data/alns/pspa_snf7.fa")
-    # tre_path=here("data/alns/pspa_snf7.tre")
-    # fasttree_path=here("src/FastTree")
     
     # Check if the FASTA file exists
     if (!file.exists(fa_path)) {
@@ -89,7 +86,7 @@ convertFA2Tree <- function(fa_path = here("data/alns/pspa_snf7.fa"),
     message(fa_path)
     system2(
         command = fasttree_path,
-        args = paste(c(fa_path, ">", tre_path),
+        args = paste(c(fa_path, ">", .data$tre_path),
             sep = "", collapse = " "
         )
     )