tests updated

ropensci · Nov 5, 2019 · 6d84fc2 · 6d84fc2
1 parent f8f439b
commit 6d84fc2
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Showing 4 changed files with 8 additions and 4 deletions.
diff --git a/tests/testthat/test-stage1.R b/tests/testthat/test-stage1.R
@@ -29,7 +29,9 @@ test_that('taxise_run() works', {
 phylotaR:::cleanup(wd)
 test_that('txids_get() works', {
   mock_search <- function(...) {
-    list('count' = 100, 'ids' = as.character(1:100))
+    res <- list('count' = 100, 'ids' = as.character(1:100))
+    class(res) <- 'esearch'
+    res
   }
   phylotaR:::cache_setup(ps)
   res <- with_mock(

diff --git a/tests/testthat/test-tools-blast.R b/tests/testthat/test-tools-blast.R
@@ -32,7 +32,7 @@ test_that('blastn_run() works', {
 test_that('outfmt_get() works', {
   res <- with_mock(
     `phylotaR:::blastdb_gen` = function(...) 0,
-    `phylotaR:::blastn_run` = function(...) 0,
+    `phylotaR:::cmdln` = function(...) 0,
     phylotaR:::outfmt_get(ps = ps)
   )
   expect_true(inherits(res, 'character'))

diff --git a/tests/testthat/test-tools-entrez.R b/tests/testthat/test-tools-entrez.R
@@ -14,7 +14,9 @@ esearch_mock <- function(db, term, retmax, retstart, ...) {
   } else {
     ids <- as.character(1:n)
   }
-  list('ids' = ids, 'count' = n)
+  res <- list('ids' = ids, 'count' = n)
+  class(res) <- 'esearch'
+  res
 }
 efetch_mock <- function(retmax, ...) {
   # when rettype == 'acc'

diff --git a/tests/testthat/test-tools-pipeline.R b/tests/testthat/test-tools-pipeline.R
@@ -35,7 +35,7 @@ test_that('parameters_setup() works', {
     phylotaR:::parameters_setup(wd = wd, txid = 9606, ncbi_execs = ncbi_execs)
   )
   ps <- phylotaR:::parameters_load(wd = wd)
-  expect_true(length(ps) == 21)
+  expect_true(length(ps) == 22)
 })
 phylotaR:::cleanup(wd)
 test_that('stage_args_check() works', {