1 files changed, 0 insertions, 196 deletions
diff --git a/skip-tests.patch b/skip-tests.patch
deleted file mode 100644
index 0d5fdbae7849..000000000000
--- a/skip-tests.patch
+++ /dev/null
@@ -1,196 +0,0 @@
-diff --git a/hermes/tests/testthat/test-calc_cor.R b/hermes/tests/testthat/test-calc_cor.R
-index f7c5f29..0010620 100644
---- a/hermes/tests/testthat/test-calc_cor.R
-+++ b/hermes/tests/testthat/test-calc_cor.R
-@@ -36,6 +36,7 @@ test_that("autoplot method does not give warnings on HermesDataCor objects", {
- })
- 
- test_that("autoplot for HermesDataCor works as expected with default options", {
-+  skip("fails")
-   object <- correlate(hermes_data)
-   result <- autoplot(object)
- 
-@@ -43,6 +44,7 @@ test_that("autoplot for HermesDataCor works as expected with default options", {
- })
- 
- test_that("autoplot for HermesDataCor works as expected with custom options", {
-+  skip("fails")
-   object <- correlate(hermes_data)
-   result <- autoplot(
-     object,
-diff --git a/hermes/tests/testthat/test-connections.R b/hermes/tests/testthat/test-connections.R
-index 7a471fa..088f659 100644
---- a/hermes/tests/testthat/test-connections.R
-+++ b/hermes/tests/testthat/test-connections.R
-@@ -2,7 +2,7 @@
- # create object `.mart` with constant Ensembl version.
- on_ci <- isTRUE(as.logical(Sys.getenv("CI")))
- on_bioc <- !(identical(Sys.getenv("BBS_HOME"), ""))
--.mart <- if (on_ci || on_bioc) {
-+.mart <- if (TRUE) {
-   NULL
- } else {
-   as(
-@@ -17,6 +17,7 @@ httr::set_config(httr::config(ssl_verifypeer = FALSE))
- # connect_biomart ----
- 
- test_that("connect_biomart works as expected", {
-+  skip("fails")
-   skip_on_ci()
-   skip_on_bioc()
- 
-@@ -30,6 +31,7 @@ test_that("connect_biomart works as expected", {
- })
- 
- test_that("connect_biomart can specify older version of Ensembl", {
-+  skip("fails")
-   skip_on_ci()
-   skip_on_bioc()
- 
-@@ -45,6 +47,7 @@ test_that("connect_biomart can specify older version of Ensembl", {
- # h_get_annotation_biomart ----
- 
- test_that("h_get_annotation_biomart works as expected", {
-+  skip("fails")
-   skip_on_ci()
-   skip_on_bioc()
- 
-@@ -86,6 +89,7 @@ test_that("h_strip_prefix works as expected", {
- # h_get_size_biomart ----
- 
- test_that("h_get_size_biomart works as expected", {
-+  skip("fails")
-   skip_on_ci()
-   skip_on_bioc()
- 
-@@ -126,6 +130,7 @@ test_that("h_get_size_biomart works as expected", {
- # h_ensembl_to_entrez_ids ----
- 
- test_that("h_ensembl_to_entrez_ids works as expected", {
-+  skip("fails")
-   skip_on_ci()
-   skip_on_bioc()
- 
-@@ -163,6 +168,7 @@ test_that("h_get_granges_by_id works as expected", {
- # query-ConnectionBiomart ----
- 
- test_that("query to Biomart works as expected", {
-+  skip("fails")
-   skip_on_ci()
-   skip_on_bioc()
- 
-diff --git a/hermes/tests/testthat/test-differential.R b/hermes/tests/testthat/test-differential.R
-index 36750a7..31198c1 100644
---- a/hermes/tests/testthat/test-differential.R
-+++ b/hermes/tests/testthat/test-differential.R
-@@ -123,6 +123,7 @@ test_that("autoplot for HermesDataDiffExpr works as expected with default option
- })
- 
- test_that("autoplot for HermesDataDiffExpr works as expected with custom options", {
-+  skip("fails")
-   colData(hermes_data) <- df_cols_to_factor(colData(hermes_data))
-   object <- diff_expression(hermes_data, "SEX", "voom")
-   result <- autoplot(object, adj_p_val_thresh = 0.92, log2_fc_thresh = 3)
-diff --git a/hermes/tests/testthat/test-draw_barplot.R b/hermes/tests/testthat/test-draw_barplot.R
-index 4c1787e..980d335 100644
---- a/hermes/tests/testthat/test-draw_barplot.R
-+++ b/hermes/tests/testthat/test-draw_barplot.R
-@@ -1,4 +1,5 @@
- test_that("draw_barplot works when there are duplicate labels in gene spec", {
-+  skip("fails")
-   genes <- gene_spec(c(A = "GeneID:11185", A = "GeneID:10677"), fun = colMeans)
-   result <- draw_barplot(
-     hermes_data,
-diff --git a/hermes/tests/testthat/test-draw_boxplot.R b/hermes/tests/testthat/test-draw_boxplot.R
-index 7e3dcf0..1da1c46 100644
---- a/hermes/tests/testthat/test-draw_boxplot.R
-+++ b/hermes/tests/testthat/test-draw_boxplot.R
-@@ -1,6 +1,7 @@
- # draw_boxplot ----
- 
- test_that("draw_boxplot works when there are duplicate labels in gene spec", {
-+  skip("fails")
-   genes <- gene_spec(c(A = "GeneID:11185", A = "GeneID:10677"))
-   result <- draw_boxplot(
-     hermes_data,
-diff --git a/hermes/tests/testthat/test-draw_scatterplot.R b/hermes/tests/testthat/test-draw_scatterplot.R
-index 8c8bf7a..c60e625 100644
---- a/hermes/tests/testthat/test-draw_scatterplot.R
-+++ b/hermes/tests/testthat/test-draw_scatterplot.R
-@@ -1,4 +1,5 @@
- test_that("draw_scatterplot works when there are duplicate labels in gene specs", {
-+  skip("fails")
-   genes_x <- gene_spec(c(A = "GeneID:11185"))
-   genes_y <- gene_spec(c(A = "GeneID:10677"))
-   result <- draw_scatterplot(
-diff --git a/hermes/tests/testthat/test-graphs.R b/hermes/tests/testthat/test-graphs.R
-index 83bd111..ef1b378 100644
---- a/hermes/tests/testthat/test-graphs.R
-+++ b/hermes/tests/testthat/test-graphs.R
-@@ -1,6 +1,7 @@
- # draw_libsize_hist ----
- 
- test_that("draw_libsize_hist works as expected", {
-+  skip("fails")
-   result <- draw_libsize_hist(hermes_data, bins = 10L, fill = "blue")
- 
-   vdiffr::expect_doppelganger("draw_libsize_hist with 10 blue bins", result)
-@@ -17,6 +18,7 @@ test_that("draw_libsize_qq works as expected", {
- # draw_libsize_densities ----
- 
- test_that("draw_libsize_densities works as expected", {
-+  skip("fails")
-   result <- draw_libsize_densities(hermes_data)
- 
-   vdiffr::expect_doppelganger("draw_libsize_densities with default log", result)
-@@ -25,6 +27,7 @@ test_that("draw_libsize_densities works as expected", {
- # draw_nonzero_boxplot ----
- 
- test_that("draw_nonzero_boxplot works as expected with default options", {
-+  skip("fails")
-   set.seed(123)
-   result <- draw_nonzero_boxplot(hermes_data)
- 
-@@ -32,6 +35,7 @@ test_that("draw_nonzero_boxplot works as expected with default options", {
- })
- 
- test_that("draw_nonzero_boxplot works as expected with custom options", {
-+  skip("fails")
-   result <- draw_nonzero_boxplot(hermes_data, position = position_identity(), alpha = 1)
- 
-   vdiffr::expect_doppelganger("draw_nonzero_boxplot with custom options", result)
-@@ -40,12 +44,14 @@ test_that("draw_nonzero_boxplot works as expected with custom options", {
- # draw_genes_barplot ----
- 
- test_that("draw_genes_barplot works as expected with default options", {
-+  skip("fails")
-   result <- draw_genes_barplot(hermes_data)
- 
-   vdiffr::expect_doppelganger("draw_genes_barplot with default options", result)
- })
- 
- test_that("draw_genes_barplot works as expected with custom options", {
-+  skip("fails")
-   result <- draw_genes_barplot(hermes_data, chromosomes = c("3", "11"), include_others = FALSE)
- 
-   vdiffr::expect_doppelganger("draw_genes_barplot with custom options", result)
-diff --git a/hermes/tests/testthat/test-top_genes.R b/hermes/tests/testthat/test-top_genes.R
-index 9e32b23..2c1712f 100644
---- a/hermes/tests/testthat/test-top_genes.R
-+++ b/hermes/tests/testthat/test-top_genes.R
-@@ -74,6 +74,7 @@ test_that("top genes gives the names of the genes in the correct order", {
- # autoplot-HermesDataTopGenes ----
- 
- test_that("autoplot for HermesDataTopGenes works as expected with default options", {
-+  skip("fails")
-   object <- top_genes(hermes_data)
-   result <- autoplot(object)
- 
-@@ -81,6 +82,7 @@ test_that("autoplot for HermesDataTopGenes works as expected with default option
- })
- 
- test_that("autoplot for HermesDataTopGenes works as expected with custom options", {
-+  skip("fails")
-   object <- top_genes(hermes_data)
-   result <- autoplot(object, x_lab = "genes", y_lab = "mean count", title = "bla")
-