[lilac] updated to 1.8.0-1

4 files changed, 67 insertions, 213 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 35c2f586a1e2..ae024cb5f9a8 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = r-hermes
 	pkgdesc = Preprocessing, analyzing, and reporting of RNA-seq data
-	pkgver = 1.6.1
+	pkgver = 1.8.0
 	pkgrel = 1
 	url = https://bioconductor.org/packages/hermes
 	arch = any
@@ -45,12 +45,11 @@ pkgbase = r-hermes
 	optdepends = r-statmod
 	optdepends = r-testthat
 	optdepends = r-vdiffr
-	optdepends = r-withr
-	source = https://bioconductor.org/packages/release/bioc/src/contrib/hermes_1.6.1.tar.gz
-	source = skip-tests.patch
-	md5sums = 9e758f81455d5fc7a8b57c3a65b4de5b
-	md5sums = e228515b639417bea13853cfc94b866a
-	b2sums = 224fd9ad63e1bdf566a41e58f90c2cd120008add812f0ff4e777d72d9c3896c7d7ed06b5759b5c5330b2126dfc0cb6097584c7650c8a1f12fd2c1dcdf34ed99c
-	b2sums = b781820238d74265dce64de9804bd568587c61c0460e15b32eabf27e0f827d673e52e852274e2613a2cf55bd54e218ad21493d78fc16f8fe954a98d3b9970bb7
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/hermes_1.8.0.tar.gz
+	source = fix-tests.patch
+	md5sums = e2a043604334a9302285e5864ecd72ab
+	md5sums = 029546b1d58fdda69b7ffa514d60f183
+	b2sums = a6264580c5c9d0591e4f5e3c0e9017e3f2666282d627beac7699d83572529646e053e5632de9ef76e615eab2226f5f0a568d22957d4bbe04d659a5f895491af3
+	b2sums = cc64529e5965906de4292e712770f226e991a549d4bf6fe9b18db1b60fcdd0a4033a9aeb9ff7c59ccf1b2fe94dc69e9e492641a9df5b8579742abf726a36083b
 
 pkgname = r-hermes
diff --git a/PKGBUILD b/PKGBUILD
index 4d0462a4a869..f49e2655b7af 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,7 +1,7 @@
 # Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
 
 _pkgname=hermes
-_pkgver=1.6.1
+_pkgver=1.8.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
 pkgrel=1
@@ -54,18 +54,17 @@ optdepends=(
   r-statmod
   r-testthat
   r-vdiffr
-  r-withr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
-        "skip-tests.patch")
-md5sums=('9e758f81455d5fc7a8b57c3a65b4de5b'
-         'e228515b639417bea13853cfc94b866a')
-b2sums=('224fd9ad63e1bdf566a41e58f90c2cd120008add812f0ff4e777d72d9c3896c7d7ed06b5759b5c5330b2126dfc0cb6097584c7650c8a1f12fd2c1dcdf34ed99c'
-        'b781820238d74265dce64de9804bd568587c61c0460e15b32eabf27e0f827d673e52e852274e2613a2cf55bd54e218ad21493d78fc16f8fe954a98d3b9970bb7')
+        "fix-tests.patch")
+md5sums=('e2a043604334a9302285e5864ecd72ab'
+         '029546b1d58fdda69b7ffa514d60f183')
+b2sums=('a6264580c5c9d0591e4f5e3c0e9017e3f2666282d627beac7699d83572529646e053e5632de9ef76e615eab2226f5f0a568d22957d4bbe04d659a5f895491af3'
+        'cc64529e5965906de4292e712770f226e991a549d4bf6fe9b18db1b60fcdd0a4033a9aeb9ff7c59ccf1b2fe94dc69e9e492641a9df5b8579742abf726a36083b')
 
 prepare() {
-  # skip failing tests
-  patch -Np1 -i skip-tests.patch
+  # fix snapshot tests
+  patch -Np1 -i fix-tests.patch
 }
 
 build() {
diff --git a/fix-tests.patch b/fix-tests.patch
new file mode 100644
index 000000000000..e3fad34e6bf5
--- /dev/null
+++ b/fix-tests.patch
@@ -0,0 +1,52 @@
+diff --git a/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-custom-options.svg b/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-custom-options.svg
+index b739901..c6f4aa1 100644
+--- a/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-custom-options.svg
++++ b/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-custom-options.svg
+@@ -18,7 +18,7 @@
+   </clipPath>
+ </defs>
+ <g clip-path='url(#cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA=)'>
+-<rect x='-0.000000000000064' y='0.00' width='720.00' height='576.00' style='stroke-width: 1.07; stroke: #FFFFFF; fill: #FFFFFF;' />
++<rect x='0.00' y='0.00' width='720.00' height='576.00' style='stroke-width: 1.07; stroke: #FFFFFF; fill: #FFFFFF;' />
+ </g>
+ <defs>
+   <clipPath id='cpMzcuNjl8NjI1Ljg5fDIyLjc4fDU0NS4xMQ=='>
+diff --git a/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-default-options.svg b/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-default-options.svg
+index 66b9399..8ff2300 100644
+--- a/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-default-options.svg
++++ b/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-default-options.svg
+@@ -18,7 +18,7 @@
+   </clipPath>
+ </defs>
+ <g clip-path='url(#cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA=)'>
+-<rect x='-0.000000000000064' y='0.00' width='720.00' height='576.00' style='stroke-width: 1.07; stroke: #FFFFFF; fill: #FFFFFF;' />
++<rect x='0.00' y='0.00' width='720.00' height='576.00' style='stroke-width: 1.07; stroke: #FFFFFF; fill: #FFFFFF;' />
+ </g>
+ <defs>
+   <clipPath id='cpMzcuNjl8NjI1Ljg5fDIyLjc4fDU0NS4xMQ=='>
+diff --git a/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-custom-options.svg b/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-custom-options.svg
+index 5fb1e94..d8fc8b1 100644
+--- a/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-custom-options.svg
++++ b/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-custom-options.svg
+@@ -54,7 +54,7 @@
+ <circle cx='378.55' cy='307.48' r='1.95' style='stroke-width: 0.71; fill: #000000;' />
+ <circle cx='378.55' cy='214.65' r='1.95' style='stroke-width: 0.71; fill: #000000;' />
+ <circle cx='378.55' cy='104.30' r='1.95' style='stroke-width: 0.71; fill: #000000;' />
+-<polygon points='364.29,528.89 392.81,528.89 392.73,528.88 393.07,528.87 393.41,528.80 393.74,528.68 394.04,528.50 394.31,528.28 394.54,528.02 394.73,527.73 394.86,527.41 394.94,527.07 394.97,526.73 394.97,526.73 394.97,516.01 394.97,516.01 394.94,515.67 394.86,515.33 394.73,515.01 394.54,514.72 394.31,514.46 394.04,514.24 393.74,514.06 393.41,513.94 393.07,513.87 392.81,513.85 364.29,513.85 364.55,513.87 364.20,513.86 363.86,513.90 363.52,513.99 363.21,514.14 362.92,514.34 362.67,514.58 362.47,514.86 362.30,515.17 362.19,515.50 362.14,515.84 362.13,516.01 362.13,526.73 362.14,526.55 362.14,526.90 362.19,527.24 362.30,527.57 362.47,527.88 362.67,528.16 362.92,528.40 363.21,528.60 363.52,528.75 363.86,528.84 364.20,528.88 ' style='stroke-width: 0.53; fill: #FFFFFF;' />
++<polygon points='364.37,528.70 392.74,528.70 392.66,528.70 392.99,528.69 393.31,528.62 393.62,528.50 393.90,528.34 394.16,528.13 394.38,527.88 394.55,527.60 394.68,527.30 394.76,526.98 394.79,526.65 394.79,526.65 394.79,516.09 394.79,516.09 394.76,515.76 394.68,515.44 394.55,515.14 394.38,514.86 394.16,514.61 393.90,514.40 393.62,514.24 393.31,514.12 392.99,514.05 392.74,514.04 364.37,514.04 364.61,514.05 364.28,514.04 363.96,514.08 363.64,514.17 363.34,514.31 363.07,514.50 362.83,514.73 362.63,514.99 362.48,515.29 362.38,515.60 362.32,515.92 362.32,516.09 362.32,526.65 362.32,526.49 362.32,526.82 362.38,527.14 362.48,527.46 362.63,527.75 362.83,528.01 363.07,528.24 363.34,528.43 363.64,528.57 363.96,528.66 364.28,528.70 ' style='stroke-width: 0.53; fill: #FFFFFF;' />
+ <text x='378.55' y='525.29' text-anchor='middle' style='font-size: 11.38px; font-family: sans;' textLength='25.64px' lengthAdjust='spacingAndGlyphs'>n=20</text>
+ <rect x='42.58' y='22.78' width='671.94' height='522.33' style='stroke-width: 1.07; stroke: #333333;' />
+ </g>
+diff --git a/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-default-options.svg b/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-default-options.svg
+index da75621..821a8d2 100644
+--- a/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-default-options.svg
++++ b/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-default-options.svg
+@@ -54,7 +54,7 @@
+ <circle cx='380.02' cy='307.69' r='1.95' style='stroke-width: 0.71; stroke: #000000; stroke-opacity: 0.25; fill: #000000; fill-opacity: 0.25;' />
+ <circle cx='361.44' cy='214.69' r='1.95' style='stroke-width: 0.71; stroke: #000000; stroke-opacity: 0.25; fill: #000000; fill-opacity: 0.25;' />
+ <circle cx='431.92' cy='104.34' r='1.95' style='stroke-width: 0.71; stroke: #000000; stroke-opacity: 0.25; fill: #000000; fill-opacity: 0.25;' />
+-<polygon points='364.29,528.89 392.81,528.89 392.73,528.88 393.07,528.87 393.41,528.80 393.74,528.68 394.04,528.50 394.31,528.28 394.54,528.02 394.73,527.73 394.86,527.41 394.94,527.07 394.97,526.73 394.97,526.73 394.97,516.01 394.97,516.01 394.94,515.67 394.86,515.33 394.73,515.01 394.54,514.72 394.31,514.46 394.04,514.24 393.74,514.06 393.41,513.94 393.07,513.87 392.81,513.85 364.29,513.85 364.55,513.87 364.20,513.86 363.86,513.90 363.52,513.99 363.21,514.14 362.92,514.34 362.67,514.58 362.47,514.86 362.30,515.17 362.19,515.50 362.14,515.84 362.13,516.01 362.13,526.73 362.14,526.55 362.14,526.90 362.19,527.24 362.30,527.57 362.47,527.88 362.67,528.16 362.92,528.40 363.21,528.60 363.52,528.75 363.86,528.84 364.20,528.88 ' style='stroke-width: 0.53; fill: #FFFFFF;' />
++<polygon points='364.37,528.70 392.74,528.70 392.66,528.70 392.99,528.69 393.31,528.62 393.62,528.50 393.90,528.34 394.16,528.13 394.38,527.88 394.55,527.60 394.68,527.30 394.76,526.98 394.79,526.65 394.79,526.65 394.79,516.09 394.79,516.09 394.76,515.76 394.68,515.44 394.55,515.14 394.38,514.86 394.16,514.61 393.90,514.40 393.62,514.24 393.31,514.12 392.99,514.05 392.74,514.04 364.37,514.04 364.61,514.05 364.28,514.04 363.96,514.08 363.64,514.17 363.34,514.31 363.07,514.50 362.83,514.73 362.63,514.99 362.48,515.29 362.38,515.60 362.32,515.92 362.32,516.09 362.32,526.65 362.32,526.49 362.32,526.82 362.38,527.14 362.48,527.46 362.63,527.75 362.83,528.01 363.07,528.24 363.34,528.43 363.64,528.57 363.96,528.66 364.28,528.70 ' style='stroke-width: 0.53; fill: #FFFFFF;' />
+ <text x='378.55' y='525.29' text-anchor='middle' style='font-size: 11.38px; font-family: sans;' textLength='25.64px' lengthAdjust='spacingAndGlyphs'>n=20</text>
+ <rect x='42.58' y='22.78' width='671.94' height='522.33' style='stroke-width: 1.07; stroke: #333333;' />
+ </g>
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")
-