conditional rhdf5 testing

cmmr · Jan 23, 2025 · 9ed94ca · 9ed94ca
1 parent e4799c8
commit 9ed94ca
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Showing 2 changed files with 13 additions and 10 deletions.
diff --git a/tests/testthat/test-read_biom.r b/tests/testthat/test-read_biom.r
@@ -8,12 +8,6 @@ test_that("read_biom", {
   expect_silent(read_biom(src = g))
   unlink(c(f, g))
 
-  f <- expect_silent(write_biom(hmp5, tempfile(), 'hdf5'))
-  g <- expect_silent(write_biom(min5, tempfile(), 'hdf5'))
-  expect_silent(read_biom(src = f))
-  expect_silent(read_biom(src = g))
-  unlink(c(f, g))
-
   f <- expect_silent(write_biom(hmp5, tempfile(fileext = '.gz'), 'tab'))
   g <- expect_silent(write_biom(min5, tempfile(fileext = '.gz'), 'tab'))
   expect_silent(read_biom(src = f))
@@ -41,4 +35,12 @@ test_that("read_biom", {
 
   expect_null(parse_json_sequences(list(rows = list(list(metadata=list())))))
   expect_null(parse_hdf5_sequences(list(observation = list(list(metadata=list())))))
+
+
+  skip_if_not_installed('rhdf5')
+  f <- expect_silent(write_biom(hmp5, tempfile(), 'hdf5'))
+  g <- expect_silent(write_biom(min5, tempfile(), 'hdf5'))
+  expect_silent(read_biom(src = f))
+  expect_silent(read_biom(src = g))
+  unlink(c(f, g))
 })
diff --git a/tests/testthat/test-write_biom.r b/tests/testthat/test-write_biom.r
@@ -14,10 +14,6 @@ test_that(desc = "write_biom", code = {
 
   skip_on_cran()
 
-  expect_silent(write_biom(hmp5, tfile, format = "hdf5"))
-  expect_silent(read_biom(tfile))
-  unlink(tfile)
-
 
   expect_silent(write_counts(hmp5, tfile));   unlink(tfile)
   expect_silent(write_metadata(hmp5, tfile)); unlink(tfile)
@@ -42,4 +38,9 @@ test_that(desc = "write_biom", code = {
   unlink(c(gzfile, bzfile))
 
 
+  skip_if_not_installed('rhdf5')
+  expect_silent(write_biom(hmp5, tfile, format = "hdf5"))
+  expect_silent(read_biom(tfile))
+  unlink(tfile)
+
 })