Description: Skip tests if required packages are not yet available in Debian.
Forwarded: TODO
Author: Dylan Aïssi

--- a/tests/testthat/test_Axt.R
+++ b/tests/testthat/test_Axt.R
@@ -69,6 +69,8 @@ test_that("test_Axt", {
 test_that("test_subAxt", {
   library(GenomicRanges)
   library(rtracklayer)
+  skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
+  skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
   tAssemblyFn <- file.path(system.file("extdata",
                                        package="BSgenome.Hsapiens.UCSC.hg38"),
                            "single_sequences.2bit")
@@ -104,6 +106,8 @@ test_that("test_subAxt", {
 # )
 
 test_that("test_fixCoordinates", {
+  skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
+  skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
   axtFnDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"),
                                  "danRer10.hg38.net.axt")
   qAssemblyFn <- file.path(system.file("extdata",
@@ -130,6 +134,8 @@ test_that("test_fixCoordinates", {
 )
 
 test_that("test_subAxt", {
+  skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
+  skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
   tAssemblyFn <- file.path(system.file("extdata",
                                        package="BSgenome.Drerio.UCSC.danRer10"),
                            "single_sequences.2bit")
@@ -156,6 +162,8 @@ test_that("test_subAxt", {
 )
 
 test_that("test_makeAxtTracks", {
+  skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
+  skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
   tAssemblyFn <- file.path(system.file("extdata",
                                        package="BSgenome.Drerio.UCSC.danRer10"),
                            "single_sequences.2bit")
--- a/tests/testthat/test_ceScan.R
+++ b/tests/testthat/test_ceScan.R
@@ -11,6 +11,9 @@ test_that("test_ceScan", {
   bedDanRer10Fn <- file.path(system.file("extdata", package="CNEr"),
                              "filter_regions.danRer10.bed")
   bedDanRer10 <- readBed(bedDanRer10Fn)
+
+  skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
+  skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
   library(BSgenome.Drerio.UCSC.danRer10)
   library(BSgenome.Hsapiens.UCSC.hg38)
   qSizesHg38 <- seqinfo(BSgenome.Hsapiens.UCSC.hg38)
@@ -49,4 +52,4 @@ test_that("test_ceScan", {
                         cigar=c("65M", "66M", "51M", "218M1D190M"))
   expect_identical(mcols(CNEHg38DanRer10[["45_50"]]), mcolsCNEs)
 }
-)
\ No newline at end of file
+)
--- a/tests/testthat/test_CNE.R
+++ b/tests/testthat/test_CNE.R
@@ -26,6 +26,8 @@ test_that("test_CNE", {
                                                            146653221)),
                                       strand="+")
   )
+  skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
+  skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
   assembly1Fn <- file.path(system.file("extdata",
                                     package="BSgenome.Drerio.UCSC.danRer10"),
                         "single_sequences.2bit")
@@ -63,4 +65,4 @@ test_that("test_CNE", {
   expect_identical(CNEMerged(cne), CNE12)
   expect_identical(CNEFinal(cne), CNE12)
 }
-)
\ No newline at end of file
+)
--- a/tests/testthat/test_GRangePairs.R
+++ b/tests/testthat/test_GRangePairs.R
@@ -99,6 +99,6 @@ test_that("test_GRangePairs", {
   expect_equal(ans$first$xmin, 117)
   expect_equal(ans$first$pars, 3.976482, tolerance=1e-5)
   expect_equal(ans$second$xmin, 111)
-  expect_equal(ans$second$pars, 3.931556, tolerance=1e-5)
+  expect_equal(ans$second$pars, 3.931556, tolerance=1e-4)
 }
 )
