From b6b237419627ef11406ff93f934eecdcfd918ea9 Mon Sep 17 00:00:00 2001
From: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: Tue, 28 Nov 2023 23:48:10 -0800
Subject: [PATCH] Further fixes to pass CHECK.

---
 DESCRIPTION                                |  3 +--
 R/saveSummarizedExperiment.R               |  6 +++++-
 tests/testthat/test-SummarizedExperiment.R | 13 ++++++++++---
 3 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0a02848..9096979 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,8 +25,7 @@ Suggests:
     rmarkdown,
     knitr,
     testthat,
-    BiocStyle,
-    jsonlite
+    BiocStyle
 VignetteBuilder: knitr
 RoxygenNote: 7.2.3
 biocViews:
diff --git a/R/saveSummarizedExperiment.R b/R/saveSummarizedExperiment.R
index c215b38..f9933b8 100644
--- a/R/saveSummarizedExperiment.R
+++ b/R/saveSummarizedExperiment.R
@@ -73,7 +73,11 @@ setMethod("saveObject", "SummarizedExperiment", function(x, path, summarizedexpe
     adir <- file.path(path, "assays")
     dir.create(adir)
     ass.names <- assayNames(x)
-    if (anyDuplicated(ass.names)) {
+    if (is.null(ass.names)) {
+        stop("assays should be named")
+    } else if (any(ass.names == "")) {
+        stop("assays should have non-empty names")
+    } else if (anyDuplicated(ass.names)) {
         stop("assays should be uniquely named")
     }
     write(toJSON(ass.names), file=file.path(adir, "names.json"))
diff --git a/tests/testthat/test-SummarizedExperiment.R b/tests/testthat/test-SummarizedExperiment.R
index 390f61b..150a3da 100644
--- a/tests/testthat/test-SummarizedExperiment.R
+++ b/tests/testthat/test-SummarizedExperiment.R
@@ -151,19 +151,26 @@ test_that("stageObject fails when the assay names are NULL or non-unique", {
     assays(se) <- ass
     expect_error(stageObject(se, tmp, "rnaseq"), "should be named")
 
+    tmp <- tempfile()
+    expect_error(saveObject(se, tmp), "should be named")
+
+    # Duplicated
     tmp <- tempfile()
     dir.create(tmp)
-    assayNames(se) <- rep("FOO", length(assayNames(se)))
+    assayNames(se) <- rep("FOO", length(assays(se)))
     expect_error(stageObject(se, tmp, "rnaseq"), "duplicate")
 
+    tmp <- tempfile()
+    expect_error(saveObject(se, tmp), "unique")
+
+    # Empty.
     tmp <- tempfile()
     dir.create(tmp)
     assayNames(se) <- c("", head(LETTERS, length(assayNames(se)) - 1))
     expect_error(stageObject(se, tmp, "rnaseq"), "empty")
 
-    # Fails in the new world.
     tmp <- tempfile()
-    expect_error(saveObject(se, tmp), "uniquely named")
+    expect_error(saveObject(se, tmp), "empty")
 })
 
 test_that("stageObject works with the various types of vectors", {