Last updated on 2020-02-19 10:48:53 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 49.16 | 174.76 | 223.92 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 35.98 | 131.76 | 167.74 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 268.91 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 262.56 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0.1 | 90.00 | 652.00 | 742.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.1 | 109.00 | 832.00 | 941.00 | OK | |
| r-patched-linux-x86_64 | 1.0.1 | 40.13 | 368.77 | 408.90 | OK | |
| r-patched-solaris-x86 | 1.0.1 | 815.00 | OK | |||
| r-release-linux-x86_64 | 1.0.1 | 38.19 | 377.13 | 415.32 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.1 | 96.00 | 601.00 | 697.00 | OK | |
| r-release-osx-x86_64 | 1.0.1 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.1 | 76.00 | 514.00 | 590.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.1 | OK |
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in 'funcy-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: accordance
> ### Title: Accordance for cluster outcomes from different methods.
> ### Aliases: accordance
>
> ### ** Examples
>
> ##Generate dataset
> k <- 3
> set.seed(2511)
> ds <- sampleFuncy(obsNr=30, timeNr=10, reg=TRUE, k=k, sd=.4)
>
> ##Cluster dataset
> res1 <- funcit(methods=1:3, data=Data(ds), k=4, clusters=Cluster(ds))
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = 1:3, data = Data(ds), k = 4, clusters = Cluster(ds))
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = 1:3, data = Data(ds), k = 4, clusters = Cluster(ds))
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x12baea48>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
Error in if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data, :
the condition has length > 1
Calls: funcit
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: tests
Result: ERROR
Running 'testthat.R' [10s/12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(funcy)
Loading required package: flexclust
Loading required package: grid
Loading required package: lattice
Loading required package: modeltools
Loading required package: stats4
Loading required package: splines
>
> test_check("funcy")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#22: silent(funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#20: test_that("All Cluster algorithms work", {
res1 <- silent(funcit(methods = methods, data = ds@data,
k = k, clusters = ds@clusters, seed = 2405, save.data = TRUE,
parallel = parallel))
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x79dc7a0>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
-- 1. Error: All Cluster algorithms work (@test-old-unit-tests.R#22) ----------
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(...)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = methods, seed = 2506, data = data, k = 4)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = methods, seed = 2506, data = data, k = 4)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#46: silent(funcit(methods = methods, seed = 2506, data = data, k = 4))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#36: test_that("Making an irregular data set regular", {
data <- expect_silent(regFuncy(ds@data, timeNr = 10, nbasis = 5,
method = "interpolate"))
data <- expect_silent(regFuncy(ds@data, baseType = "splines",
timeNr = 10, nbasis = 10, method = "project")$data)
res2 <- silent(funcit(methods = methods, seed = 2506, data = data,
k = 4))
cl <- lapply(res2@models, class)
expected <- structure(c("funcyOutMbc-fitfclust", "funcyOut",
"funcyOut-iterSubspace", "funcyOutMbc", "funcyOutMbc-fscm",
"funcyOutMbc"), .Names = c("fitfclust", "distclust",
"iterSubspace", "funHDDC", "fscm", "waveclust"))
expect_equal(object = unlist(cl), expected = expected)
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x79dc7a0>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
-- 2. Error: Making an irregular data set regular (@test-old-unit-tests.R#46) -
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(methods = methods, seed = 2506, data = data, k = 4)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#76: silent(funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#65: test_that("Test control arguments", {
k <- 4
set.seed(3806)
ds <- sampleFuncy(timeNrMin = 5, timeNrMax = 10, reg = FALSE,
k = k, sd = 0.3)
a <- list(coeffsCalc = "estimate", average = TRUE)
fpcCtrl <- as(a, "fpcCtrl")
b <- list(maxit = 5, baseType = "eigenbasis", flexDim = TRUE)
funcyCtrlMbc <- as(b, "funcyCtrlMbc")
res3 <- silent(funcit(methods = c(1, 2, 3), data = ds@data,
k = k, clusters = ds@clusters, fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc,
save.data = TRUE, parallel = parallel))
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x79dc7a0>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
-- 3. Error: Test control arguments (@test-old-unit-tests.R#76) ---------------
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(...)
== testthat results ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Error: All Cluster algorithms work (@test-old-unit-tests.R#22)
2. Error: Making an irregular data set regular (@test-old-unit-tests.R#46)
3. Error: Test control arguments (@test-old-unit-tests.R#76)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: accordance
> ### Title: Accordance for cluster outcomes from different methods.
> ### Aliases: accordance
>
> ### ** Examples
>
> ##Generate dataset
> k <- 3
> set.seed(2511)
> ds <- sampleFuncy(obsNr=30, timeNr=10, reg=TRUE, k=k, sd=.4)
>
> ##Cluster dataset
> res1 <- funcit(methods=1:3, data=Data(ds), k=4, clusters=Cluster(ds))
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = 1:3, data = Data(ds), k = 4, clusters = Cluster(ds))
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = 1:3, data = Data(ds), k = 4, clusters = Cluster(ds))
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x55ea57ab6008>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
Error in if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data, :
the condition has length > 1
Calls: funcit
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(funcy)
Loading required package: flexclust
Loading required package: grid
Loading required package: lattice
Loading required package: modeltools
Loading required package: stats4
Loading required package: splines
>
> test_check("funcy")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#22: silent(funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#20: test_that("All Cluster algorithms work", {
res1 <- silent(funcit(methods = methods, data = ds@data,
k = k, clusters = ds@clusters, seed = 2405, save.data = TRUE,
parallel = parallel))
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x55b1f2a55080>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
── 1. Error: All Cluster algorithms work (@test-old-unit-tests.R#22) ──────────
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(...)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = methods, seed = 2506, data = data, k = 4)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = methods, seed = 2506, data = data, k = 4)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#46: silent(funcit(methods = methods, seed = 2506, data = data, k = 4))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#36: test_that("Making an irregular data set regular", {
data <- expect_silent(regFuncy(ds@data, timeNr = 10, nbasis = 5,
method = "interpolate"))
data <- expect_silent(regFuncy(ds@data, baseType = "splines",
timeNr = 10, nbasis = 10, method = "project")$data)
res2 <- silent(funcit(methods = methods, seed = 2506, data = data,
k = 4))
cl <- lapply(res2@models, class)
expected <- structure(c("funcyOutMbc-fitfclust", "funcyOut",
"funcyOut-iterSubspace", "funcyOutMbc", "funcyOutMbc-fscm",
"funcyOutMbc"), .Names = c("fitfclust", "distclust",
"iterSubspace", "funHDDC", "fscm", "waveclust"))
expect_equal(object = unlist(cl), expected = expected)
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x55b1f2a55080>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
── 2. Error: Making an irregular data set regular (@test-old-unit-tests.R#46) ─
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(methods = methods, seed = 2506, data = data, k = 4)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#76: silent(funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#65: test_that("Test control arguments", {
k <- 4
set.seed(3806)
ds <- sampleFuncy(timeNrMin = 5, timeNrMax = 10, reg = FALSE,
k = k, sd = 0.3)
a <- list(coeffsCalc = "estimate", average = TRUE)
fpcCtrl <- as(a, "fpcCtrl")
b <- list(maxit = 5, baseType = "eigenbasis", flexDim = TRUE)
funcyCtrlMbc <- as(b, "funcyCtrlMbc")
res3 <- silent(funcit(methods = c(1, 2, 3), data = ds@data,
k = k, clusters = ds@clusters, fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc,
save.data = TRUE, parallel = parallel))
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x55b1f2a55080>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
── 3. Error: Test control arguments (@test-old-unit-tests.R#76) ───────────────
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(...)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Error: All Cluster algorithms work (@test-old-unit-tests.R#22)
2. Error: Making an irregular data set regular (@test-old-unit-tests.R#46)
3. Error: Test control arguments (@test-old-unit-tests.R#76)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:
> ### Name: accordance
> ### Title: Accordance for cluster outcomes from different methods.
> ### Aliases: accordance
>
> ### ** Examples
>
> ##Generate dataset
> k <- 3
> set.seed(2511)
> ds <- sampleFuncy(obsNr=30, timeNr=10, reg=TRUE, k=k, sd=.4)
>
> ##Cluster dataset
> res1 <- funcit(methods=1:3, data=Data(ds), k=4, clusters=Cluster(ds))
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = 1:3, data = Data(ds), k = 4, clusters = Cluster(ds))
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = 1:3, data = Data(ds), k = 4, clusters = Cluster(ds))
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0xb7080a0>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
Error in if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data, :
the condition has length > 1
Calls: funcit
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
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(funcy)
Loading required package: flexclust
Loading required package: grid
Loading required package: lattice
Loading required package: modeltools
Loading required package: stats4
Loading required package: splines
>
> test_check("funcy")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#22: silent(funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#20: test_that("All Cluster algorithms work", {
res1 <- silent(funcit(methods = methods, data = ds@data,
k = k, clusters = ds@clusters, seed = 2405, save.data = TRUE,
parallel = parallel))
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x7fada10>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
── 1. Error: All Cluster algorithms work (@test-old-unit-tests.R#22) ──────────
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(...)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = methods, seed = 2506, data = data, k = 4)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = methods, seed = 2506, data = data, k = 4)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#46: silent(funcit(methods = methods, seed = 2506, data = data, k = 4))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#36: test_that("Making an irregular data set regular", {
data <- expect_silent(regFuncy(ds@data, timeNr = 10, nbasis = 5,
method = "interpolate"))
data <- expect_silent(regFuncy(ds@data, baseType = "splines",
timeNr = 10, nbasis = 10, method = "project")$data)
res2 <- silent(funcit(methods = methods, seed = 2506, data = data,
k = 4))
cl <- lapply(res2@models, class)
expected <- structure(c("funcyOutMbc-fitfclust", "funcyOut",
"funcyOut-iterSubspace", "funcyOutMbc", "funcyOutMbc-fscm",
"funcyOutMbc"), .Names = c("fitfclust", "distclust",
"iterSubspace", "funHDDC", "fscm", "waveclust"))
expect_equal(object = unlist(cl), expected = expected)
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x7fada10>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
── 2. Error: Making an irregular data set regular (@test-old-unit-tests.R#46) ─
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(methods = methods, seed = 2506, data = data, k = 4)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#76: silent(funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#65: test_that("Test control arguments", {
k <- 4
set.seed(3806)
ds <- sampleFuncy(timeNrMin = 5, timeNrMax = 10, reg = FALSE,
k = k, sd = 0.3)
a <- list(coeffsCalc = "estimate", average = TRUE)
fpcCtrl <- as(a, "fpcCtrl")
b <- list(maxit = 5, baseType = "eigenbasis", flexDim = TRUE)
funcyCtrlMbc <- as(b, "funcyCtrlMbc")
res3 <- silent(funcit(methods = c(1, 2, 3), data = ds@data,
k = k, clusters = ds@clusters, fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc,
save.data = TRUE, parallel = parallel))
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x7fada10>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
── 3. Error: Test control arguments (@test-old-unit-tests.R#76) ───────────────
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(...)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Error: All Cluster algorithms work (@test-old-unit-tests.R#22)
2. Error: Making an irregular data set regular (@test-old-unit-tests.R#46)
3. Error: Test control arguments (@test-old-unit-tests.R#76)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:
> ### Name: accordance
> ### Title: Accordance for cluster outcomes from different methods.
> ### Aliases: accordance
>
> ### ** Examples
>
> ##Generate dataset
> k <- 3
> set.seed(2511)
> ds <- sampleFuncy(obsNr=30, timeNr=10, reg=TRUE, k=k, sd=.4)
>
> ##Cluster dataset
> res1 <- funcit(methods=1:3, data=Data(ds), k=4, clusters=Cluster(ds))
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = 1:3, data = Data(ds), k = 4, clusters = Cluster(ds))
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = 1:3, data = Data(ds), k = 4, clusters = Cluster(ds))
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x123be6d0>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
Error in if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data, :
the condition has length > 1
Calls: funcit
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
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(funcy)
Loading required package: flexclust
Loading required package: grid
Loading required package: lattice
Loading required package: modeltools
Loading required package: stats4
Loading required package: splines
>
> test_check("funcy")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#22: silent(funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,
seed = 2405, save.data = TRUE, parallel = parallel))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#20: test_that("All Cluster algorithms work", {
res1 <- silent(funcit(methods = methods, data = ds@data,
k = k, clusters = ds@clusters, seed = 2405, save.data = TRUE,
parallel = parallel))
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x8cd7fc8>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
── 1. Error: All Cluster algorithms work (@test-old-unit-tests.R#22) ──────────
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(...)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = methods, seed = 2506, data = data, k = 4)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = methods, seed = 2506, data = data, k = 4)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#46: silent(funcit(methods = methods, seed = 2506, data = data, k = 4))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#36: test_that("Making an irregular data set regular", {
data <- expect_silent(regFuncy(ds@data, timeNr = 10, nbasis = 5,
method = "interpolate"))
data <- expect_silent(regFuncy(ds@data, baseType = "splines",
timeNr = 10, nbasis = 10, method = "project")$data)
res2 <- silent(funcit(methods = methods, seed = 2506, data = data,
k = 4))
cl <- lapply(res2@models, class)
expected <- structure(c("funcyOutMbc-fitfclust", "funcyOut",
"funcyOut-iterSubspace", "funcyOutMbc", "funcyOutMbc-fscm",
"funcyOutMbc"), .Names = c("fitfclust", "distclust",
"iterSubspace", "funHDDC", "fscm", "waveclust"))
expect_equal(object = unlist(cl), expected = expected)
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x8cd7fc8>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
── 2. Error: Making an irregular data set regular (@test-old-unit-tests.R#46) ─
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(methods = methods, seed = 2506, data = data, k = 4)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
funcy
--- call from context ---
funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel)
--- call from argument ---
if (!(class(data) %in% c("matrix", "data.frame"))) stop(paste(data,
"must be given in matrix or data.frame format."))
--- R stacktrace ---
where 1: funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel)
where 2: eval(expr, pf)
where 3: eval(expr, pf)
where 4: withVisible(eval(expr, pf))
where 5: evalVis(expr)
where 6 at testthat/test-old-unit-tests.R#7: capture.output(result <- expr)
where 7 at testthat/test-old-unit-tests.R#76: silent(funcit(methods = c(1, 2, 3), data = ds@data, k = k, clusters = ds@clusters,
fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc, save.data = TRUE,
parallel = parallel))
where 8: eval(code, test_env)
where 9: eval(code, test_env)
where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 16: tryCatchList(expr, classes, parentenv, handlers)
where 17: 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 18: test_code(desc, code, env = parent.frame())
where 19 at testthat/test-old-unit-tests.R#65: test_that("Test control arguments", {
k <- 4
set.seed(3806)
ds <- sampleFuncy(timeNrMin = 5, timeNrMax = 10, reg = FALSE,
k = k, sd = 0.3)
a <- list(coeffsCalc = "estimate", average = TRUE)
fpcCtrl <- as(a, "fpcCtrl")
b <- list(maxit = 5, baseType = "eigenbasis", flexDim = TRUE)
funcyCtrlMbc <- as(b, "funcyCtrlMbc")
res3 <- silent(funcit(methods = c(1, 2, 3), data = ds@data,
k = k, clusters = ds@clusters, fpcCtrl = fpcCtrl, funcyCtrl = funcyCtrlMbc,
save.data = TRUE, parallel = parallel))
})
where 20: eval(code, test_env)
where 21: eval(code, test_env)
where 22: 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 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: test_code(NULL, exprs, env)
where 31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 32: force(code)
where 33: doWithOneRestart(return(expr), restart)
where 34: withOneRestart(expr, restarts[[1L]])
where 35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 36: 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 37: FUN(X[[i]], ...)
where 38: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 39: force(code)
where 40: doWithOneRestart(return(expr), restart)
where 41: withOneRestart(expr, restarts[[1L]])
where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 43: 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 44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 45: 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 46: 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 47: test_check("funcy")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, k, methods = c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust"), seed = NULL,
regTime = NULL, clusters = NULL, funcyCtrl = NULL, fpcCtrl = NULL,
parallel = FALSE, save.data = TRUE, ...)
{
if (missing(methods))
stop("Please select one method or methods='ALL'.")
else if (length(methods) == 1)
if (methods == "ALL")
methods <- 1:7
allMethods <- c("fitfclust", "distclust", "iterSubspace",
"funclust", "funHDDC", "fscm", "waveclust")
if (is.numeric(methods))
usedMethods <- allMethods[methods]
else usedMethods <- match.arg(methods, allMethods, several.ok = TRUE)
nrMethods <- length(usedMethods)
if (missing(k))
stop(paste(k, "is missing"))
if (!(class(data) %in% c("matrix", "data.frame")))
stop(paste(data, "must be given in matrix or data.frame format."))
chf <- checkFormat(data)
data <- chf$data
reg <- chf$reg
if (is.null(funcyCtrl))
funcyCtrl <- new("funcyCtrl")
funcyCtrl@seed <- seed
if (sum(usedMethods %in% allMethods[c(1, 3, 4, 5, 6, 7)]) >
0 & class(funcyCtrl) == "funcyCtrl")
funcyCtrl <- as(funcyCtrl, "funcyCtrlMbc")
if (funcyCtrl@baseType != "eigenbasis" & !is.null(fpcCtrl))
warning("fpcCtrl is ignored since it controls only eigenbasis.")
else if (funcyCtrl@baseType == "eigenbasis")
fpcCtrl <- fpcCtrlCheck(fpcCtrl = fpcCtrl, data = data,
reg = reg)
if (reg == 0 & sum(usedMethods %in% c("fscm", "funclust",
"funHDDC")) > 0) {
notWork <- usedMethods[which(usedMethods %in% allMethods[-c(1:3)])]
stop(paste("Algorithm", notWork, "works only on regular data!\n Please choose one of fitfclust, distclust or iterSubspace."))
}
if (nrMethods == 1)
parallel <- FALSE
if (.Platform$OS.type != "unix" & parallel) {
warning("Parallel computing is only supported on Unix platforms.")
parallel <- FALSE
}
if (parallel) {
parallelFct <- parallel::mcparallel
coresNr <- detectCores() - 1
options(cores = coresNr)
}
else {
parallelFct <- identity
}
RES <- list()
if ("fitfclust" %in% usedMethods) {
indx <- match("fitfclust", usedMethods)
RES[[indx]] <- parallelFct(fitfclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("distclust" %in% usedMethods) {
indx <- match("distclust", usedMethods)
RES[[indx]] <- parallelFct(distclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrl = funcyCtrl, ...))
}
if ("iterSubspace" %in% usedMethods) {
indx <- match("iterSubspace", usedMethods)
RES[[indx]] <- parallelFct(iterSubspaceWrapper(data = data,
k = k, reg = reg, regTime = regTime, fpcCtrl = fpcCtrl,
funcyCtrlMbc = funcyCtrl, ...))
}
if ("funclust" %in% usedMethods) {
.warn_once <- local({
not.warned.yet <- TRUE
function(x) {
if (not.warned.yet) {
warning("Funclustering is currently not available on CRAN.")
not.warned.yet <<- FALSE
}
}
})
}
if ("funHDDC" %in% usedMethods) {
if (!requireNamespace("funHDDC"))
stop("Please install package 'funHDDC' to use method 'funHDDC'.")
indx <- match("funHDDC", usedMethods)
RES[[indx]] <- parallelFct(funHDDCWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("fscm" %in% usedMethods) {
indx <- match("fscm", usedMethods)
RES[[indx]] <- parallelFct(fscmWrapper(data = data, k = k,
reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
if ("waveclust" %in% usedMethods) {
indx <- match("waveclust", usedMethods)
RES[[indx]] <- parallelFct(waveclustWrapper(data = data,
k = k, reg = reg, regTime = regTime, funcyCtrlMbc = funcyCtrl,
...))
}
FRES <- new("funcyOutList")
FRES@call <- match.call()
if (parallel)
FRES@models <- parallel::mccollect(RES)
else FRES@models <- RES
names(FRES@models) <- usedMethods
error <- which(sapply(FRES@models, class) == "try-error")
if (sum(error) != 0)
stop(paste("Method", usedMethods[error[1]], ":", attributes(FRES@models[[error[1]]])$condition$message))
allClusters <- sapply(FRES@models, function(x) x@cluster)
allCenters <- lapply(FRES@models, function(x) x@centers)
names(allCenters) <- colnames(allClusters) <- usedMethods
rI <- rIMethods(methodNames = usedMethods, cls = allClusters,
trueCluster = clusters)
if (nrMethods > 1) {
rel <- relabelMethods(methodNames = usedMethods, cls = allClusters,
ctrs = allCenters)
allClusters <- rel$allClusters
allCenters <- rel$allCenters
for (i in 1:nrMethods) {
FRES@models[[i]]@cluster <- allClusters[, i]
FRES@models[[i]]@centers <- allCenters[[i]]
FRES@models[[i]]@correctCl <- rI[i, i]
}
}
smallCl <- which(apply(allClusters, 2, function(x) min(table(x))) <
2)
if (length(smallCl) != 0) {
warning(paste("Method", usedMethods[smallCl], "has clusters with less than 3 obervations!\n"),
immediate. = TRUE)
}
accord <- accordance(cls = allClusters, relabel = FALSE)
if (save.data)
FRES@data <- data
else FRES@data <- as.matrix(NULL)
FRES@timeNr <- calcTimeNr(data, reg)
FRES@reg <- reg
FRES@k <- k
FRES@methodName <- usedMethods
FRES@allClusters <- allClusters
FRES@randIndex <- rI
FRES@votedCluster <- accord$votedCluster
FRES@accordance <- accord$accordance
return(FRES)
}
<bytecode: 0x8cd7fc8>
<environment: namespace:funcy>
--- function search by body ---
Function funcit in namespace funcy has this body.
----------- END OF FAILURE REPORT --------------
── 3. Error: Test control arguments (@test-old-unit-tests.R#76) ───────────────
the condition has length > 1
Backtrace:
1. funcy:::silent(...)
7. funcy::funcit(...)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Error: All Cluster algorithms work (@test-old-unit-tests.R#22)
2. Error: Making an irregular data set regular (@test-old-unit-tests.R#46)
3. Error: Test control arguments (@test-old-unit-tests.R#76)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc