increase timeout

mmollina · Dec 18, 2023 · e48dfd5 · e48dfd5
1 parent 4ac2175
commit e48dfd5
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Showing 8 changed files with 27 additions and 22 deletions.
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -23,7 +23,7 @@ jobs:
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-renv@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: covr
 

diff --git a/R/functions_qtl.R b/R/functions_qtl.R
@@ -195,7 +195,7 @@ only_plot_profile <- function(pl.in){
     geom_line(data=pl.in$lines, aes(y = SIG, color = Trait), linewidth=pl.in$linesize, alpha=0.8) +
     #guides(color = guide_legend("Trait")) + 
     {if(dim(pl.in$points)[1] > 0) geom_point(data=pl.in$points, aes(y = y.dat, color = Trait), shape = 2, size = 2, stroke = 1, alpha = 0.8)} +
-    {if(length(vlines) > 1) geom_vline(xintercept=vlines, linetype="dashed", size=.5, alpha=0.8, na.rm = TRUE)} +  #threshold
+    {if(length(vlines) > 1) geom_vline(xintercept=vlines, linetype="dashed", linewidth=.5, alpha=0.8, na.rm = TRUE)} +  #threshold
     labs(y = pl.in$y.lab, x = "Linkage group") +
     annotate(x=vlines,y=+Inf,label= paste0("LG", names(vlines)),vjust=1, hjust= -0.1,geom="label") +
     ylim(c(min(pl.in$lines$y.dat),max(pl.in$lines$SIG, na.rm = T) + 3)) +
@@ -466,9 +466,9 @@ data_effects <- function(qtl_info, effects, pheno.col = NULL,
       for(i in 1:length(pheno.col.n)){
         p[[i]] <- effects.df %>% filter(.data$pheno == unique(qtl_info$pheno)[pheno.col.n][i]) %>%  
           ggplot() +
-          geom_path(aes(x=x.axis, y=haplo, col = effect), size = 5)  +
+          geom_path(aes(x=x.axis, y=haplo, col = effect), linewidth = 5)  +
           scale_color_gradient2(low = "purple4", mid = "white",high = "seagreen") +
-          {if(length(vlines) > 1) geom_vline(xintercept=vlines, linetype="dashed", size=.5, alpha=0.8, na.rm = TRUE)} +
+          {if(length(vlines) > 1) geom_vline(xintercept=vlines, linetype="dashed", linewidth=.5, alpha=0.8, na.rm = TRUE)} +
           labs(y = "Haplotype", x = "Linkage group", title = unique(qtl_info$pheno)[pheno.col.n][i]) +
           annotate(x=vlines,y=+Inf,label= paste0("LG", names(vlines)),vjust= 1, hjust= -0.1,geom="label") +
           coord_cartesian(ylim = c(1,8.5)) +

diff --git a/tests/testthat/test-MAPpoly.R b/tests/testthat/test-MAPpoly.R
@@ -4,6 +4,7 @@ test_that("Tests uploaded MAPpoly files",{
   # upload MAPpoly
   temp <- tempfile()
   if(havingIP()){
+    options(timeout=200)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_MAPpoly_maps.RData", destfile = temp)
     temp.name <- load(temp)
     input.data <- get(temp.name)
@@ -29,7 +30,7 @@ test_that("Tests uploaded MAPpoly files",{
                              ch = 3,
                              maps = maps,
                              d.p1 = viewmap_mappoly$d.p1,
-                             d.p2 = viewmap_mappoly$d.p2)[[5]], 134.073, tolerance = 0.0001, )
+                             d.p2 = viewmap_mappoly$d.p2)[[5]], 134.073, tolerance = 0.0001)
 
     # Map summary table
     summary_table <- summary_maps(viewmap_mappoly, software = "mappoly")

diff --git a/tests/testthat/test-QTLpoly.R b/tests/testthat/test-QTLpoly.R
@@ -9,6 +9,7 @@ test_that("Tests uploaded QTLpoly files",{
   fitted.mod$datapath <- tempfile()
 
   if(havingIP()){
+    options(timeout=200)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_QTLpoly_effects.RData", destfile = est.effects$datapath)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_QTLpoly_data.RData", destfile = input.data$datapath)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_QTLpoly_remim.RData", destfile = remim.mod$datapath)

diff --git a/tests/testthat/test-diaQTL.R b/tests/testthat/test-diaQTL.R
@@ -9,6 +9,7 @@ test_that("Tests uploaded diaQTL files",{
   BayesCI_list_temp$datapath <- tempfile()
 
   if(havingIP()){
+    options(timeout=200)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_diaQTL_BayesCI_list_0.RData", destfile = BayesCI_list_temp$datapath)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_diaQTL_scan1_list.RData", destfile = scan1_list$datapath)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_diaQTL_scan1_summaries_list.RData", destfile = scan1_summaries_list$datapath)

diff --git a/tests/testthat/test-polymapR.R b/tests/testthat/test-polymapR.R
@@ -7,6 +7,7 @@ test_that("Tests uploaded polymapR files",{
   polymapR.map$datapath <- tempfile()
 
   if(havingIP()){
+    options(timeout=200)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_polymapR_dataset.RData", destfile = input.data$datapath)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_polymapR_map.RData", destfile = polymapR.map$datapath)
 

diff --git a/tests/testthat/test-polyqtlR.R b/tests/testthat/test-polyqtlR.R
@@ -8,6 +8,7 @@ test_that("Tests uploaded polyqtlR files",{
   polyqtlR_effects$datapath <- tempfile()
 
   if(havingIP()){
+    options(timeout=200)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_polyqtlR_qtl_info.RData", destfile = polyqtlR_qtl_info$datapath)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_polyqtlR_QTLscan.RData", destfile = polyqtlR_QTLscan_list$datapath)
     download.file("https://www.polyploids.org/sites/default/files/2022-04/tetra_polyqtlR_effects.RData", destfile = polyqtlR_effects$datapath)

diff --git a/tests/testthat/test-tetra_example.R b/tests/testthat/test-tetra_example.R
@@ -2,9 +2,9 @@ test_that("tetra example",{
   source(system.file("ext/functions4tests.R", package = "viewpoly"))
 
   # upload examples
-  viewpoly_obj <- viewpoly:::prepare_examples("tetra_map")
+  viewpoly_obj <- prepare_examples("tetra_map")
 
-  expect_equal(viewpoly:::check_viewpoly(viewpoly_obj),0)
+  expect_equal(check_viewpoly(viewpoly_obj),0)
 
   check_viewmap_values(viewpoly_obj$map,
                        c(14, 132, 139, 157, 34),
@@ -21,7 +21,7 @@ test_that("tetra example",{
                                1)
 
   # VIEWmap tests
-  qtl_profile_plot <- viewpoly:::plot_profile(profile = viewpoly_obj$qtl$profile,
+  qtl_profile_plot <- plot_profile(profile = viewpoly_obj$qtl$profile,
                                               qtl_info = viewpoly_obj$qtl$qtl_info,
                                               selected_mks = viewpoly_obj$qtl$selected_mks,
                                               pheno.col = 2:3,
@@ -60,10 +60,10 @@ test_that("tetra example",{
                                                                          ph.p2 = viewpoly_obj$map$ph.p2,
                                                                          snp.names = TRUE, software = "mappoly"))
 
-  vdiffr::expect_doppelganger("plot map list", viewpoly:::plot_map_list(viewpoly_obj$map))
+  vdiffr::expect_doppelganger("plot map list", plot_map_list(viewpoly_obj$map))
 
   # Get max size each chromosome
-  expect_equal(viewpoly:::map_summary(left.lim = 1,
+  expect_equal(map_summary(left.lim = 1,
                                       right.lim = 50,
                                       ch = 3,
                                       maps = maps,
@@ -78,7 +78,7 @@ test_that("tetra example",{
   expect_equal(sum(as.numeric(summary_table$`Max gap`)), 80.51)
 
   #VIEWqtl tests
-  vdiffr::expect_doppelganger("qtl plot", viewpoly:::plot_profile(viewpoly_obj$qtl$profile,
+  vdiffr::expect_doppelganger("qtl plot", plot_profile(viewpoly_obj$qtl$profile,
                                                                   viewpoly_obj$qtl$qtl_info,
                                                                   viewpoly_obj$qtl$selected_mks,
                                                                   pheno.col = 2,
@@ -88,7 +88,7 @@ test_that("tetra example",{
                                                                   software = NULL))
 
   # by range
-  qtl_profile_data <- viewpoly:::plot_profile(viewpoly_obj$qtl$profile,
+  qtl_profile_data <- plot_profile(viewpoly_obj$qtl$profile,
                                               viewpoly_obj$qtl$qtl_info,
                                               viewpoly_obj$qtl$selected_mks,
                                               pheno.col = 2,
@@ -107,7 +107,7 @@ test_that("tetra example",{
   expect_equal(as.numeric(qtl_profile_data$points$SUP), 119, tolerance = 0.001)
 
   # export data
-  qtl_profile_data <- viewpoly:::plot_profile(viewpoly_obj$qtl$profile,
+  qtl_profile_data <- plot_profile(viewpoly_obj$qtl$profile,
                                               viewpoly_obj$qtl$qtl_info,
                                               viewpoly_obj$qtl$selected_mks,
                                               pheno.col = 2,
@@ -126,11 +126,11 @@ test_that("tetra example",{
   expect_equal(as.numeric(qtl_profile_data$points$SUP), 119, tolerance = 0.001)
 
   # plot exported data
-  p <- viewpoly:::only_plot_profile(qtl_profile_data)
+  p <- only_plot_profile(qtl_profile_data)
   expect_equal(sum(p$data$SIG), 292.883, tolerance = 0.001)
 
   # effects graphics
-  p <- viewpoly:::data_effects(qtl_info = viewpoly_obj$qtl$qtl_info,
+  p <- data_effects(qtl_info = viewpoly_obj$qtl$qtl_info,
                                effects = viewpoly_obj$qtl$effects,
                                pheno.col = "SG06",
                                lgs = 2,
@@ -139,7 +139,7 @@ test_that("tetra example",{
                                software = "QTLpoly",
                                design = "circle")
 
-  vdiffr::expect_doppelganger("effects circle", viewpoly:::plot_effects(data_effects.obj = p,
+  vdiffr::expect_doppelganger("effects circle", plot_effects(data_effects.obj = p,
                                                                         software = "QTLpoly",
                                                                         design = "circle"))
 
@@ -148,7 +148,7 @@ test_that("tetra example",{
                c("Estimates", "Alleles", "Parent", "Effects", "pheno", "qtl_id", "LG", "Pos", "unique.id"),
                tolerance = 0.001)
 
-  p <- viewpoly:::data_effects(qtl_info = viewpoly_obj$qtl$qtl_info,
+  p <- data_effects(qtl_info = viewpoly_obj$qtl$qtl_info,
                                effects = viewpoly_obj$qtl$effects,
                                pheno.col = "SG06",
                                lgs = 2,
@@ -162,9 +162,9 @@ test_that("tetra example",{
                c("x", "y", "z"),
                tolerance = 0.001)
 
-  vdiffr::expect_doppelganger("effects digenic", viewpoly:::plot_effects(p, "QTLpoly", "digenic"))
+  vdiffr::expect_doppelganger("effects digenic", plot_effects(p, "QTLpoly", "digenic"))
 
-  p <- viewpoly:::data_effects(qtl_info = viewpoly_obj$qtl$qtl_info,
+  p <- data_effects(qtl_info = viewpoly_obj$qtl$qtl_info,
                                effects = viewpoly_obj$qtl$effects,
                                pheno.col = "SG06",
                                lgs = 2,
@@ -178,11 +178,11 @@ test_that("tetra example",{
                c("Estimates", "Alleles", "Parent", "Effects"),
                tolerance = 0.001)
 
-  vdiffr::expect_doppelganger("effects bar", viewpoly:::plot_effects(p, "QTLpoly", "bar"))
+  vdiffr::expect_doppelganger("effects bar", plot_effects(p, "QTLpoly", "bar"))
 
   # breeding values table
   pos <- split(viewpoly_obj$qtl$qtl_info[1:3,]$Pos, viewpoly_obj$qtl$qtl_info[1:3,]$pheno)
-  breed.values <- viewpoly:::breeding_values(viewpoly_obj$qtl$qtl_info,
+  breed.values <- breeding_values(viewpoly_obj$qtl$qtl_info,
                                              viewpoly_obj$qtl$probs,
                                              viewpoly_obj$qtl$selected_mks,
                                              viewpoly_obj$qtl$blups,
@@ -211,7 +211,7 @@ test_that("tetra example",{
   expect_equal(sum(p1[[3]]$data$probability), 508.0009, tolerance = 0.0001)
 
   # VIEWgenome tests
-  p <- viewpoly:::plot_cm_mb(viewpoly_obj$map, 1, 1,50)
+  p <- plot_cm_mb(viewpoly_obj$map, 1, 1,50)
 
   expect_equal(sum(p$data$l.dist), 50502.07, tolerance = 0.001)