From aff579c128a954f34d98ca3550183fdaf71ddc24 Mon Sep 17 00:00:00 2001 From: "p.aboyoun" Date: Fri, 26 Mar 2010 05:24:40 +0000 Subject: [PATCH] Move to new testing paradigm. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@45528 bc3139a8-67e5-0310-9ffc-ced21a209358 --- DESCRIPTION | 1 + R/test_GenomicRanges_package.R | 48 +++++++++++++++++++ .../unitTests/test_GRanges-class.R | 0 .../unitTests/test_GRangesList-class.R | 0 .../unitTests/test_GappedAlignments-class.R | 0 .../unitTests/test_cigar-utils.R | 0 .../unitTests/test_findOverlaps.R | 0 .../unitTests/test_setops.R | 0 tests/GenomicRanges_unit_tests.R | 2 + tests/runalltests.R | 18 ------- tests/runalltests.Rout.save | 35 -------------- 11 files changed, 51 insertions(+), 53 deletions(-) create mode 100644 R/test_GenomicRanges_package.R rename tests/unit/GRanges-class_test.R => inst/unitTests/test_GRanges-class.R (100%) rename tests/unit/GRangesList-class_test.R => inst/unitTests/test_GRangesList-class.R (100%) rename tests/unit/GappedAlignments-class_test.R => inst/unitTests/test_GappedAlignments-class.R (100%) rename tests/unit/cigar-utils_test.R => inst/unitTests/test_cigar-utils.R (100%) rename tests/unit/findOverlaps_test.R => inst/unitTests/test_findOverlaps.R (100%) rename tests/unit/setops_test.R => inst/unitTests/test_setops.R (100%) create mode 100644 tests/GenomicRanges_unit_tests.R delete mode 100644 tests/runalltests.R delete mode 100644 tests/runalltests.Rout.save diff --git a/DESCRIPTION b/DESCRIPTION index 4d4aebd..7861853 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -26,3 +26,4 @@ Collate: seqnames.R Alignments0-class.R Alignments1-class.R Alignments2-class.R + test_GenomicRanges_package.R diff --git a/R/test_GenomicRanges_package.R b/R/test_GenomicRanges_package.R new file mode 100644 index 0000000..639ddda --- /dev/null +++ b/R/test_GenomicRanges_package.R @@ -0,0 +1,48 @@ +.test <- function(dir, pattern = "^test_.*\\.R$") +{ + .failure_details <- function(result) { + res <- result[[1L]] + if (res$nFail > 0 || res$nErr > 0) { + Filter(function(x) length(x) > 0, + lapply(res$sourceFileResults, + function(fileRes) { + names(Filter(function(x) x$kind != "success", + fileRes)) + })) + } else list() + } + + if (missing(dir)) { + dir <- system.file("unitTests", package="GenomicRanges") + if (!length(dir)) { + dir <- system.file("UnitTests", package="GenomicRanges") + if (!length(dir)) + stop("unable to find unit tests, no 'unitTests' dir") + } + } + require("RUnit", quietly=TRUE) || stop("RUnit package not found") + RUnit_opts <- getOption("RUnit", list()) + RUnit_opts$verbose <- 0L + RUnit_opts$silent <- TRUE + RUnit_opts$verbose_fail_msg <- TRUE + options(RUnit = RUnit_opts) + suite <- defineTestSuite(name="GenomicRanges RUnit Tests", dirs=dir, + testFileRegexp=pattern, + rngKind="default", + rngNormalKind="default") + result <- runTestSuite(suite) + cat("\n\n") + printTextProtocol(result, showDetails=FALSE) + if (length(details <- .failure_details(result)) >0) { + cat("\nTest files with failing tests\n") + for (i in seq_along(details)) { + cat("\n ", basename(names(details)[[i]]), "\n") + for (j in seq_along(details[[i]])) { + cat(" ", details[[i]][[j]], "\n") + } + } + cat("\n\n") + stop("unit tests failed for package GenomicRanges") + } + result +} diff --git a/tests/unit/GRanges-class_test.R b/inst/unitTests/test_GRanges-class.R similarity index 100% rename from tests/unit/GRanges-class_test.R rename to inst/unitTests/test_GRanges-class.R diff --git a/tests/unit/GRangesList-class_test.R b/inst/unitTests/test_GRangesList-class.R similarity index 100% rename from tests/unit/GRangesList-class_test.R rename to inst/unitTests/test_GRangesList-class.R diff --git a/tests/unit/GappedAlignments-class_test.R b/inst/unitTests/test_GappedAlignments-class.R similarity index 100% rename from tests/unit/GappedAlignments-class_test.R rename to inst/unitTests/test_GappedAlignments-class.R diff --git a/tests/unit/cigar-utils_test.R b/inst/unitTests/test_cigar-utils.R similarity index 100% rename from tests/unit/cigar-utils_test.R rename to inst/unitTests/test_cigar-utils.R diff --git a/tests/unit/findOverlaps_test.R b/inst/unitTests/test_findOverlaps.R similarity index 100% rename from tests/unit/findOverlaps_test.R rename to inst/unitTests/test_findOverlaps.R diff --git a/tests/unit/setops_test.R b/inst/unitTests/test_setops.R similarity index 100% rename from tests/unit/setops_test.R rename to inst/unitTests/test_setops.R diff --git a/tests/GenomicRanges_unit_tests.R b/tests/GenomicRanges_unit_tests.R new file mode 100644 index 0000000..0890fbb --- /dev/null +++ b/tests/GenomicRanges_unit_tests.R @@ -0,0 +1,2 @@ +require("GenomicRanges") || stop("unable to load GenomicRanges package") +GenomicRanges:::.test() diff --git a/tests/runalltests.R b/tests/runalltests.R deleted file mode 100644 index 43b280e..0000000 --- a/tests/runalltests.R +++ /dev/null @@ -1,18 +0,0 @@ -suppressMessages(library("GenomicRanges")) -suppressMessages(library("RUnit")) - -options(warn=1) - -dirs <- 'unit' - -testFilePat <- ".*_test\\.R$" - -allSuite <- defineTestSuite(name="allSuite", - dirs=dirs, - testFileRegexp=testFilePat, - rngKind="default", - rngNormalKind="default") - -results <- capture.output(runTestSuite(allSuite)) - -q(runLast=FALSE) diff --git a/tests/runalltests.Rout.save b/tests/runalltests.Rout.save deleted file mode 100644 index 2b675aa..0000000 --- a/tests/runalltests.Rout.save +++ /dev/null @@ -1,35 +0,0 @@ - -R version 2.9.0 Under development (unstable) (--) -Copyright (C) The R Foundation for Statistical Computing -ISBN 3-900051-07-0 - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> suppressMessages(library("GenomicRanges")) -> suppressMessages(library("RUnit")) -> -> options(warn=1) -> -> dirs <- 'unit' -> -> testFilePat <- ".*_test\\.R$" -> -> allSuite <- defineTestSuite(name="allSuite", -+ dirs=dirs, -+ testFileRegexp=testFilePat, -+ rngKind="default", -+ rngNormalKind="default") -> -> results <- capture.output(runTestSuite(allSuite)) -> -> q(runLast=FALSE)