suppress warnings from read_biom which caused check error

yiluheihei · Nov 3, 2023 · e4fea2f · e4fea2f
1 parent a8b677e
commit e4fea2f
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -60,7 +60,7 @@ Imports:
     pROC,
     BiocParallel
 Encoding: UTF-8
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Suggests: 
     testthat,

diff --git a/R/import-qiime2.R b/R/import-qiime2.R
@@ -160,7 +160,7 @@ read_qza <- function(file, temp = tempdir()) {
 #' @return [`phyloseq::otu_table-class`] object.
 #' @noRd
 read_q2biom <- function(file) {
-    biomobj <- read_biom(file)
+    biomobj <- suppressWarnings(read_biom(file))
     feature_tab <- as(biom_data(biomobj), "matrix")
 
     otu_table(feature_tab, taxa_are_rows = TRUE)
@@ -215,7 +215,7 @@ parse_q2taxonomy <- function(taxa, sep = "; |;", trim_rank_prefix = TRUE) {
         taxa$Taxon <- gsub("D_\\d__", "", taxa$Taxon)
     }
 
-    taxa <- tidyr::separate(taxa, .data$Taxon, 
+    taxa <- tidyr::separate(taxa, .data$Taxon,
         c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
         sep = sep,
         fill = "right"