tests update

GreenleafLab · Jul 19, 2022 · 56025dd · 56025dd
1 parent 606e699
commit 56025dd
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Showing 12 changed files with 22 additions and 9 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/man/addCoAccessibility.Rd b/man/addCoAccessibility.Rd
diff --git a/man/addGeneScoreMatrix.Rd b/man/addGeneScoreMatrix.Rd
diff --git a/man/addIterativeLSI.Rd b/man/addIterativeLSI.Rd
diff --git a/man/addMotifAnnotations.Rd b/man/addMotifAnnotations.Rd
diff --git a/man/createArrowFiles.Rd b/man/createArrowFiles.Rd
diff --git a/man/getPeak2GeneLinks.Rd b/man/getPeak2GeneLinks.Rd
diff --git a/man/plotPeak2GeneHeatmap.Rd b/man/plotPeak2GeneHeatmap.Rd
diff --git a/tests/testthat/test_5_chromVAR.R → tests/testthat/test_2_chromVAR.R b/tests/testthat/test_5_chromVAR.R → tests/testthat/test_2_chromVAR.R
@@ -29,7 +29,7 @@ matches <- getMatches(proj)
 stopifnot(all(paste0(rowRanges(se))==paste0(rowRanges(matches))))
 
 #Background Peaks
-se2 <- SummarizedExperiment(assays=SimpleList(counts=cbind(rowSums(assay(se)), 1)))
+se2 <- SummarizedExperiment(assays=SimpleList(counts=cbind(Matrix::rowSums(assay(se)), 1)))
 rowRanges(se2) <- rowRanges(se)
 bgdPeaks <- getBackgroundPeaks(se2)
 
@@ -91,3 +91,16 @@ test_that("Testing ArchR ChromVAR", {
   expect_equal(all(corZ_23 > 0.99), TRUE)
 })
 
+################################################
+# Clear
+################################################
+
+files <- list.files()
+files <- files[!grepl("\\.R", files)]
+for(i in seq_along(files)){
+  if(dir.exists(files[i])){
+    unlink(files[i], recursive=TRUE)
+  }else if(file.exists(files[i])){
+    file.remove(files[i])
+  }
+}
diff --git a/tests/testthat/test_4_cpp.R → tests/testthat/test_3_cpp.R b/tests/testthat/test_4_cpp.R → tests/testthat/test_3_cpp.R
diff --git a/tests/testthat/test_2_worklow.R → tests/testthat/test_4_worklow.R b/tests/testthat/test_2_worklow.R → tests/testthat/test_4_worklow.R
diff --git a/tests/testthat/test_3_rd.R → tests/testthat/test_5_rd.R b/tests/testthat/test_3_rd.R → tests/testthat/test_5_rd.R