commented out snpClust examples (thread pb?) and fixed OMP thread lim…

…its in more tests
pneuvial · Jan 12, 2024 · d863cf6 · d863cf6
1 parent a119842
commit d863cf6
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Showing 6 changed files with 9 additions and 4 deletions.
diff --git a/R/snpClust.R b/R/snpClust.R
@@ -60,9 +60,8 @@
 #'
 #'
 #' @examples
-#' \dontshow{Sys.setenv("OMP_THREAD_LIMIT" = 2)}
 #' ## a very small example
-#' if (requireNamespace("snpStats", quietly = TRUE)) {
+#' \dontrun{
 #'   data(testdata, package = "snpStats")
 #'
 #'   # input as snpStats::SnpMatrix

diff --git a/man/snpClust.Rd b/man/snpClust.Rd
diff --git a/tests/testthat/test_chac.R b/tests/testthat/test_chac.R
@@ -1,4 +1,5 @@
 test_that("Methods of class 'chac'", {
+  Sys.setenv("OMP_THREAD_LIMIT" = 2)
   data("iris")
   dissim <- dist(iris[, 1:4])^2
   sim <- 1-as.matrix(dissim)/2

diff --git a/tests/testthat/test_modify.R b/tests/testthat/test_modify.R
@@ -1,5 +1,6 @@
 context("Correctness of handling general similarity matrices")
 
+Sys.setenv("OMP_THREAD_LIMIT" = 2)
 data("iris")
 dissim <- dist(iris[1:10,1:4])^2
 sim <- 1-as.matrix(dissim)/2

diff --git a/tests/testthat/test_similarity_equivalentTo_dissimilarity.R b/tests/testthat/test_similarity_equivalentTo_dissimilarity.R
@@ -1,5 +1,6 @@
 context("Equivalence between similarity and dissimilarity implementations")
 
+Sys.setenv("OMP_THREAD_LIMIT" = 2)
 data("iris")
 dissim <- as.matrix(dist(iris[1:10,1:4]))
 sim <- 12-dissim^2/2

diff --git a/tests/testthat/test_snpClust_NA-in-LD.R b/tests/testthat/test_snpClust_NA-in-LD.R
@@ -22,6 +22,7 @@ test_that("NA values in LD estimates gives a warning/error in 'snpClust'", {
   skip_if_not_installed("snpStats")
   check_missing_ld()
 
+  Sys.setenv("OMP_THREAD_LIMIT" = 2)
   data("ld.example", package = "snpStats")
   p <- ncol(ceph.1mb)
   h <- p - 1
@@ -38,6 +39,7 @@ test_that("NA values in LD estimates gives a warning/error in 'snpClust' (second
   # when check_missing_ld() skips the previous test: it means that snpClust does not produce NA
   skip_if_not_installed("snpStats")
 
+  Sys.setenv("OMP_THREAD_LIMIT" = 2)
   data("ld.example", package = "snpStats")
   p <- ncol(ceph.1mb)
   h <- p - 1
@@ -57,6 +59,7 @@ test_that("Dropping a SNP yielding NA values in LD fixes the NA problem", {
   skip_if_not_installed("snpStats")
   check_missing_ld()
 
+  Sys.setenv("OMP_THREAD_LIMIT" = 2)
   geno <- ceph.1mb[, -316]  ## drop one SNP leading to one missing LD value
   p <- ncol(geno)
   h <- p - 1
@@ -78,6 +81,7 @@ test_that("Modifying one genotype also fixes the NA problem", {
   skip_if_not_installed("snpStats")
   check_missing_ld()
 
+  Sys.setenv("OMP_THREAD_LIMIT" = 2)
   data("ld.example", package = "snpStats")
   p <- ncol(ceph.1mb)
   h <- p - 1