CRAN Package Check Results for Package DGCA

Last updated on 2019-11-26 00:51:49 CET.

Check Details

Version: 1.0.1
Check: tests
Result: ERROR
     Running 'testthat.R' [13s/16s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(DGCA)
    
     > test_check("DGCA")
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     DGCA
     --- call from context ---
     getCors(cbind(t(simData_A2), t(simData_B2)), design_mat)
     --- call from argument ---
     if (!class(inputMat) %in% c("data.frame", "matrix")) stop("Input data should be either data.frame or matrix.\n")
     --- R stacktrace ---
     where 1 at testthat/test-dCorrs.R#50: getCors(cbind(t(simData_A2), t(simData_B2)), design_mat)
     where 2: eval(code, test_env)
     where 3: eval(code, test_env)
     where 4: withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error)
     where 5: doTryCatch(return(expr), name, parentenv, handler)
     where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 8: doTryCatch(return(expr), name, parentenv, handler)
     where 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 10: tryCatchList(expr, classes, parentenv, handlers)
     where 11: tryCatch(withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error), error = handle_fatal,
     skip = function(e) {
     })
     where 12: test_code(desc, code, env = parent.frame())
     where 13 at testthat/test-dCorrs.R#26: test_that("pairwiseDCor works", {
     simData_A2 = simData_A
     simData_B2 = simData_B
     simData_A2[, 1] = c(2, 1.1, rep(1, times = (nrows - 2)))
     simData_A2[, 2] = c(0, rep(1, times = (nrows - 1)))
     simData_B2[, 1] = c(2, 1.1, rep(1, times = (nrows - 2)))
     simData_B2[, 2] = c(2, rep(1, times = (nrows - 1)))
     expect_equal(round(matCorr(simData_B2, corrType = "pearson")[1,
     2], digits = 2), 0.99)
     expect_equal(round(matCorr(simData_B2, corrType = "spearman")[1,
     2], digits = 2), 0.76)
     fac = factor(c(rep("A", times = nrow(simData_A2)), rep("B",
     times = nrow(simData_B2))))
     design_mat = model.matrix(~fac + 0)
     cor_res = getCors(cbind(t(simData_A2), t(simData_B2)), design_mat)
     PDC = pairwiseDCor(cor_res, compare = c("facA", "facB"))
     expect_equal(round(slot(PDC, "ZDiff")[1, 2], 0), 9)
     expect_equal(round(log(slot(PDC, "PValDiff")[1, 2], 10),
     0), -18)
     expect_error(pairwiseDCor(cor_res, compare = c("foo", "bar")),
     "names are not in")
     dc_slice = dcTopPairs(PDC, 40, classify = FALSE)
     expect_equal(dc_slice[1, "Gene2"], col_names[2])
     expect_equal(round(dc_slice[1, "zScoreDiff"], 0), 9)
     expect_equal(round(log(dc_slice[1, "pValDiff"], 10), 0),
     -18)
     dc_slice_class = dcTopPairs(PDC, 40, classify = TRUE)
     expect_equal(as.character(dc_slice_class[1, "Classes"]),
     "-/+")
     dc_top = dcTopPairs(PDC, nPairs = 30)
     expect_equal(as.character(dc_top[1, c("Gene1", "Gene2")]),
     c(col_names[1], col_names[2]))
     })
     where 14: eval(code, test_env)
     where 15: eval(code, test_env)
     where 16: withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error)
     where 17: doTryCatch(return(expr), name, parentenv, handler)
     where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 20: doTryCatch(return(expr), name, parentenv, handler)
     where 21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 22: tryCatchList(expr, classes, parentenv, handlers)
     where 23: tryCatch(withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error), error = handle_fatal,
     skip = function(e) {
     })
     where 24: test_code(NULL, exprs, env)
     where 25: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 26: force(code)
     where 27: doWithOneRestart(return(expr), restart)
     where 28: withOneRestart(expr, restarts[[1L]])
     where 29: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 30: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
     {
     reporter$start_file(basename(path))
     lister$start_file(basename(path))
     source_file(path, new.env(parent = env), chdir = TRUE,
     wrap = wrap)
     reporter$.end_context()
     reporter$end_file()
     })
     where 31: FUN(X[[i]], ...)
     where 32: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 33: force(code)
     where 34: doWithOneRestart(return(expr), restart)
     where 35: withOneRestart(expr, restarts[[1L]])
     where 36: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 37: with_reporter(reporter = current_reporter, results <- lapply(paths,
     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
     load_helpers = FALSE, wrap = wrap))
     where 38: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 39: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
     wrap = wrap)
     where 40: test_package_dir(package = package, test_path = test_path, filter = filter,
     reporter = reporter, ..., stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 41: test_check("DGCA")
    
     --- value of length: 2 type: logical ---
     [1] FALSE TRUE
     --- function from context ---
     function (inputMat, design, inputMatB = NULL, impute = FALSE,
     corrType = "pearson")
     {
     SAF = getOption("stringsAsFactors")
     on.exit(options(stringsAsFactors = SAF))
     options(stringsAsFactors = FALSE)
     if (!corrType %in% c("pearson", "spearman"))
     stop("corrType should be one of \"pearson\" or \"spearman\".\n")
     if (!class(inputMat) %in% c("data.frame", "matrix"))
     stop("Input data should be either data.frame or matrix.\n")
     if (!mode(design) == "numeric")
     stop("Design matrix must be numeric.\n")
     if (!all(design %in% c(0, 1)))
     stop("Design matrix must be made up of 0's and 1's.\n")
     if (nrow(design) != ncol(inputMat))
     stop("The number of rows in the design matrix must be equal to the number of columns in the input matrix.")
     if (!is.null(inputMatB)) {
     if (nrow(design) != ncol(inputMatB))
     stop("The number of rows in the design matrix must be equal to the number of columns in the input matrix.")
     if (!class(inputMatB) %in% c("data.frame", "matrix"))
     stop("Input data should be either data.frame or matrix.\n")
     }
     if (impute == TRUE) {
     if (!requireNamespace("impute", quietly = TRUE)) {
     stop("The R package impute is needed for the impute knn function to work. Please install it.",
     call. = FALSE)
     }
     if (any(is.na(inputMat))) {
     imputed = impute::impute.knn(as.matrix(inputMat))
     inputMat = imputed$data
     }
     else {
     message("No NA values in input, so ignoring impute = TRUE.\n")
     }
     if (!is.null(inputMatB)) {
     if (any(is.na(inputMatB))) {
     imputedB = impute::impute.knn(as.matrix(inputMatB))
     inputMatB = imputedB$data
     }
     else {
     message("No NA values in secondary input, so ignoring impute = TRUE.\n")
     }
     }
     }
     if (is.null(inputMatB)) {
     designRes = getGroupsFromDesign(inputMat, design)
     groupList = designRes[[1]]
     groupMatLists = as.list(rep(NA, length(groupList)))
     names(groupMatLists) = designRes[[2]]
     for (i in 1:length(groupList)) {
     corr = matCorr(t(groupList[[i]]), corrType = corrType)
     nsamp = matNSamp(t(groupList[[i]]), impute = impute)
     pval = matCorSig(corr, nsamp)
     groupMatLists[[i]] = list(corrs = corr, pvals = pval,
     nsamps = nsamp)
     }
     }
     if (!is.null(inputMatB)) {
     designRes = getGroupsFromDesign(inputMat = inputMat,
     design = design, inputMatB = inputMatB, secondMat = TRUE)
     groupListA = designRes[[1]]
     groupListB = designRes[[2]]
     groupMatLists = as.list(rep(NA, length(groupListA)))
     names(groupMatLists) = designRes[[3]]
     for (i in 1:length(groupListA)) {
     corr = matCorr(matA = t(groupListA[[i]]), corrType = corrType,
     matB = t(groupListB[[i]]), secondMat = TRUE)
     nsamp = matNSamp(matA = t(groupListA[[i]]), impute = impute,
     matB = t(groupListB[[i]]), secondMat = TRUE)
     pval = matCorSig(corr, nsamp, secondMat = TRUE)
     groupMatLists[[i]] = list(corrs = corr, pvals = pval,
     nsamps = nsamp)
     }
     }
     options = c(corrType)
     names(options) = c("corrType")
     corMatsObj = new("corMats", corMatList = groupMatLists, design = design,
     options = options)
     return(corMatsObj)
     }
     <bytecode: 0x10888678>
     <environment: namespace:DGCA>
     --- function search by body ---
     Function getCors in namespace DGCA has this body.
     ----------- END OF FAILURE REPORT --------------
     Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [10s/16s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(DGCA)
    
     > test_check("DGCA")
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     DGCA
     --- call from context ---
     getCors(cbind(t(simData_A2), t(simData_B2)), design_mat)
     --- call from argument ---
     if (!class(inputMat) %in% c("data.frame", "matrix")) stop("Input data should be either data.frame or matrix.\n")
     --- R stacktrace ---
     where 1 at testthat/test-dCorrs.R#50: getCors(cbind(t(simData_A2), t(simData_B2)), design_mat)
     where 2: eval(code, test_env)
     where 3: eval(code, test_env)
     where 4: withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error)
     where 5: doTryCatch(return(expr), name, parentenv, handler)
     where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 8: doTryCatch(return(expr), name, parentenv, handler)
     where 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 10: tryCatchList(expr, classes, parentenv, handlers)
     where 11: tryCatch(withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error), error = handle_fatal,
     skip = function(e) {
     })
     where 12: test_code(desc, code, env = parent.frame())
     where 13 at testthat/test-dCorrs.R#26: test_that("pairwiseDCor works", {
     simData_A2 = simData_A
     simData_B2 = simData_B
     simData_A2[, 1] = c(2, 1.1, rep(1, times = (nrows - 2)))
     simData_A2[, 2] = c(0, rep(1, times = (nrows - 1)))
     simData_B2[, 1] = c(2, 1.1, rep(1, times = (nrows - 2)))
     simData_B2[, 2] = c(2, rep(1, times = (nrows - 1)))
     expect_equal(round(matCorr(simData_B2, corrType = "pearson")[1,
     2], digits = 2), 0.99)
     expect_equal(round(matCorr(simData_B2, corrType = "spearman")[1,
     2], digits = 2), 0.76)
     fac = factor(c(rep("A", times = nrow(simData_A2)), rep("B",
     times = nrow(simData_B2))))
     design_mat = model.matrix(~fac + 0)
     cor_res = getCors(cbind(t(simData_A2), t(simData_B2)), design_mat)
     PDC = pairwiseDCor(cor_res, compare = c("facA", "facB"))
     expect_equal(round(slot(PDC, "ZDiff")[1, 2], 0), 9)
     expect_equal(round(log(slot(PDC, "PValDiff")[1, 2], 10),
     0), -18)
     expect_error(pairwiseDCor(cor_res, compare = c("foo", "bar")),
     "names are not in")
     dc_slice = dcTopPairs(PDC, 40, classify = FALSE)
     expect_equal(dc_slice[1, "Gene2"], col_names[2])
     expect_equal(round(dc_slice[1, "zScoreDiff"], 0), 9)
     expect_equal(round(log(dc_slice[1, "pValDiff"], 10), 0),
     -18)
     dc_slice_class = dcTopPairs(PDC, 40, classify = TRUE)
     expect_equal(as.character(dc_slice_class[1, "Classes"]),
     "-/+")
     dc_top = dcTopPairs(PDC, nPairs = 30)
     expect_equal(as.character(dc_top[1, c("Gene1", "Gene2")]),
     c(col_names[1], col_names[2]))
     })
     where 14: eval(code, test_env)
     where 15: eval(code, test_env)
     where 16: withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error)
     where 17: doTryCatch(return(expr), name, parentenv, handler)
     where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 20: doTryCatch(return(expr), name, parentenv, handler)
     where 21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 22: tryCatchList(expr, classes, parentenv, handlers)
     where 23: tryCatch(withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error), error = handle_fatal,
     skip = function(e) {
     })
     where 24: test_code(NULL, exprs, env)
     where 25: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 26: force(code)
     where 27: doWithOneRestart(return(expr), restart)
     where 28: withOneRestart(expr, restarts[[1L]])
     where 29: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 30: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
     {
     reporter$start_file(basename(path))
     lister$start_file(basename(path))
     source_file(path, new.env(parent = env), chdir = TRUE,
     wrap = wrap)
     reporter$.end_context()
     reporter$end_file()
     })
     where 31: FUN(X[[i]], ...)
     where 32: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 33: force(code)
     where 34: doWithOneRestart(return(expr), restart)
     where 35: withOneRestart(expr, restarts[[1L]])
     where 36: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 37: with_reporter(reporter = current_reporter, results <- lapply(paths,
     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
     load_helpers = FALSE, wrap = wrap))
     where 38: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 39: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
     wrap = wrap)
     where 40: test_package_dir(package = package, test_path = test_path, filter = filter,
     reporter = reporter, ..., stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 41: test_check("DGCA")
    
     --- value of length: 2 type: logical ---
     [1] FALSE TRUE
     --- function from context ---
     function (inputMat, design, inputMatB = NULL, impute = FALSE,
     corrType = "pearson")
     {
     SAF = getOption("stringsAsFactors")
     on.exit(options(stringsAsFactors = SAF))
     options(stringsAsFactors = FALSE)
     if (!corrType %in% c("pearson", "spearman"))
     stop("corrType should be one of \"pearson\" or \"spearman\".\n")
     if (!class(inputMat) %in% c("data.frame", "matrix"))
     stop("Input data should be either data.frame or matrix.\n")
     if (!mode(design) == "numeric")
     stop("Design matrix must be numeric.\n")
     if (!all(design %in% c(0, 1)))
     stop("Design matrix must be made up of 0's and 1's.\n")
     if (nrow(design) != ncol(inputMat))
     stop("The number of rows in the design matrix must be equal to the number of columns in the input matrix.")
     if (!is.null(inputMatB)) {
     if (nrow(design) != ncol(inputMatB))
     stop("The number of rows in the design matrix must be equal to the number of columns in the input matrix.")
     if (!class(inputMatB) %in% c("data.frame", "matrix"))
     stop("Input data should be either data.frame or matrix.\n")
     }
     if (impute == TRUE) {
     if (!requireNamespace("impute", quietly = TRUE)) {
     stop("The R package impute is needed for the impute knn function to work. Please install it.",
     call. = FALSE)
     }
     if (any(is.na(inputMat))) {
     imputed = impute::impute.knn(as.matrix(inputMat))
     inputMat = imputed$data
     }
     else {
     message("No NA values in input, so ignoring impute = TRUE.\n")
     }
     if (!is.null(inputMatB)) {
     if (any(is.na(inputMatB))) {
     imputedB = impute::impute.knn(as.matrix(inputMatB))
     inputMatB = imputedB$data
     }
     else {
     message("No NA values in secondary input, so ignoring impute = TRUE.\n")
     }
     }
     }
     if (is.null(inputMatB)) {
     designRes = getGroupsFromDesign(inputMat, design)
     groupList = designRes[[1]]
     groupMatLists = as.list(rep(NA, length(groupList)))
     names(groupMatLists) = designRes[[2]]
     for (i in 1:length(groupList)) {
     corr = matCorr(t(groupList[[i]]), corrType = corrType)
     nsamp = matNSamp(t(groupList[[i]]), impute = impute)
     pval = matCorSig(corr, nsamp)
     groupMatLists[[i]] = list(corrs = corr, pvals = pval,
     nsamps = nsamp)
     }
     }
     if (!is.null(inputMatB)) {
     designRes = getGroupsFromDesign(inputMat = inputMat,
     design = design, inputMatB = inputMatB, secondMat = TRUE)
     groupListA = designRes[[1]]
     groupListB = designRes[[2]]
     groupMatLists = as.list(rep(NA, length(groupListA)))
     names(groupMatLists) = designRes[[3]]
     for (i in 1:length(groupListA)) {
     corr = matCorr(matA = t(groupListA[[i]]), corrType = corrType,
     matB = t(groupListB[[i]]), secondMat = TRUE)
     nsamp = matNSamp(matA = t(groupListA[[i]]), impute = impute,
     matB = t(groupListB[[i]]), secondMat = TRUE)
     pval = matCorSig(corr, nsamp, secondMat = TRUE)
     groupMatLists[[i]] = list(corrs = corr, pvals = pval,
     nsamps = nsamp)
     }
     }
     options = c(corrType)
     names(options) = c("corrType")
     corMatsObj = new("corMats", corMatList = groupMatLists, design = design,
     options = options)
     return(corMatsObj)
     }
     <bytecode: 0x562bd42c88e0>
     <environment: namespace:DGCA>
     --- function search by body ---
     Function getCors in namespace DGCA has this body.
     ----------- END OF FAILURE REPORT --------------
     Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'doMC'
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘WGCNA’
    
    Package suggested but not available for checking: ‘org.Hs.eg.db’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64