Last updated on 2019-12-01 07:55:50 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.2 | 103.53 | 174.51 | 278.04 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.2 | 62.36 | 137.78 | 200.14 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.2 | 377.91 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.2 | 349.54 | OK | |||
| r-devel-windows-ix86+x86_64 | 1.0.2 | 185.00 | 339.00 | 524.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.2 | 206.00 | 284.00 | 490.00 | OK | |
| r-patched-linux-x86_64 | 1.0.2 | 67.64 | 177.29 | 244.93 | OK | |
| r-patched-solaris-x86 | 1.0.2 | 356.50 | OK | |||
| r-release-linux-x86_64 | 1.0.2 | 68.44 | 180.03 | 248.47 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.2 | 148.00 | 331.00 | 479.00 | OK | |
| r-release-osx-x86_64 | 1.0.2 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.2 | 191.00 | 438.00 | 629.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.2 | OK |
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in 'Quartet-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CompareQuartets
> ### Title: Compare quartet states by explicit enumeration
> ### Aliases: CompareQuartets
>
> ### ** Examples
>
> n_tip <- 6
> trees <- list(ape::rtree(n_tip, tip.label=seq_len(n_tip), br=NULL),
+ ape::rtree(n_tip, tip.label=seq_len(n_tip), br=NULL))
> splits <- lapply(trees, TreeSearch::Tree2Splits)
> quartets <- QuartetStates(splits)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
Quartet
--- call from context ---
QuartetStates(splits)
--- call from argument ---
if (class(splits[[1]]) == "phylo") splits <- lapply(splits, Tree2Splits)
--- R stacktrace ---
where 1: QuartetStates(splits)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (splits)
{
if (class(splits) == "phylo") {
splits <- list(Tree2Splits(splits))
}
else if (class(splits) == "multiPhylo") {
splits <- lapply(splits, Tree2Splits)
}
if (class(splits) != "list")
splits <- list(splits)
if (class(splits[[1]]) == "phylo")
splits <- lapply(splits, Tree2Splits)
n_tips <- dim(splits[[1]])[1]
lapply(splits, function(bips) {
vapply(AllQuartets(n_tips), QuartetState, double(1),
bips = bips[sort(rownames(bips)), , drop = FALSE])
})
}
<bytecode: 0xcc554d8>
<environment: namespace:Quartet>
--- function search by body ---
Function QuartetStates in namespace Quartet has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: tests
Result: ERROR
Running 'testthat.R' [7s/8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(Quartet)
>
> test_check("Quartet")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
Quartet
--- call from context ---
QuartetStates(quartets[[1]])
--- call from argument ---
if (class(splits[[1]]) == "phylo") splits <- lapply(splits, Tree2Splits)
--- R stacktrace ---
where 1: QuartetStates(quartets[[1]])
where 2: eval_bare(expr, quo_get_env(quo))
where 3: quasi_label(enquo(expected), expected.label, arg = "expected")
where 4 at testthat/test-QuartetDistance.R#14: expect_equal(list(2L), QuartetStates(quartets[[1]]))
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: 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 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: 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 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-QuartetDistance.R#13: test_that("QuartetStates works", {
expect_equal(list(2L), QuartetStates(quartets[[1]]))
expect_equal(list(3L), QuartetStates(Tree2Splits(quartets[[2]])))
expect_equal(list(2L, 3L, 4L, 0L), QuartetStates(quartets))
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: 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 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: 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 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: 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 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: 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 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: 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 43: 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 44: test_check("Quartet")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (splits)
{
if (class(splits) == "phylo") {
splits <- list(Tree2Splits(splits))
}
else if (class(splits) == "multiPhylo") {
splits <- lapply(splits, Tree2Splits)
}
if (class(splits) != "list")
splits <- list(splits)
if (class(splits[[1]]) == "phylo")
splits <- lapply(splits, Tree2Splits)
n_tips <- dim(splits[[1]])[1]
lapply(splits, function(bips) {
vapply(AllQuartets(n_tips), QuartetState, double(1),
bips = bips[sort(rownames(bips)), , drop = FALSE])
})
}
<bytecode: 0xd957a70>
<environment: namespace:Quartet>
--- function search by body ---
Function QuartetStates in namespace Quartet has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in ‘Quartet-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CompareQuartets
> ### Title: Compare quartet states by explicit enumeration
> ### Aliases: CompareQuartets
>
> ### ** Examples
>
> n_tip <- 6
> trees <- list(ape::rtree(n_tip, tip.label=seq_len(n_tip), br=NULL),
+ ape::rtree(n_tip, tip.label=seq_len(n_tip), br=NULL))
> splits <- lapply(trees, TreeSearch::Tree2Splits)
> quartets <- QuartetStates(splits)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
Quartet
--- call from context ---
QuartetStates(splits)
--- call from argument ---
if (class(splits[[1]]) == "phylo") splits <- lapply(splits, Tree2Splits)
--- R stacktrace ---
where 1: QuartetStates(splits)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (splits)
{
if (class(splits) == "phylo") {
splits <- list(Tree2Splits(splits))
}
else if (class(splits) == "multiPhylo") {
splits <- lapply(splits, Tree2Splits)
}
if (class(splits) != "list")
splits <- list(splits)
if (class(splits[[1]]) == "phylo")
splits <- lapply(splits, Tree2Splits)
n_tips <- dim(splits[[1]])[1]
lapply(splits, function(bips) {
vapply(AllQuartets(n_tips), QuartetState, double(1),
bips = bips[sort(rownames(bips)), , drop = FALSE])
})
}
<bytecode: 0x55c5bc6810a8>
<environment: namespace:Quartet>
--- function search by body ---
Function QuartetStates in namespace Quartet has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(Quartet)
>
> test_check("Quartet")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
Quartet
--- call from context ---
QuartetStates(quartets[[1]])
--- call from argument ---
if (class(splits[[1]]) == "phylo") splits <- lapply(splits, Tree2Splits)
--- R stacktrace ---
where 1: QuartetStates(quartets[[1]])
where 2: eval_bare(expr, quo_get_env(quo))
where 3: quasi_label(enquo(expected), expected.label, arg = "expected")
where 4 at testthat/test-QuartetDistance.R#14: expect_equal(list(2L), QuartetStates(quartets[[1]]))
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: 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 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: 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 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-QuartetDistance.R#13: test_that("QuartetStates works", {
expect_equal(list(2L), QuartetStates(quartets[[1]]))
expect_equal(list(3L), QuartetStates(Tree2Splits(quartets[[2]])))
expect_equal(list(2L, 3L, 4L, 0L), QuartetStates(quartets))
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: 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 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: 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 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: 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 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: 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 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: 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 43: 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 44: test_check("Quartet")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (splits)
{
if (class(splits) == "phylo") {
splits <- list(Tree2Splits(splits))
}
else if (class(splits) == "multiPhylo") {
splits <- lapply(splits, Tree2Splits)
}
if (class(splits) != "list")
splits <- list(splits)
if (class(splits[[1]]) == "phylo")
splits <- lapply(splits, Tree2Splits)
n_tips <- dim(splits[[1]])[1]
lapply(splits, function(bips) {
vapply(AllQuartets(n_tips), QuartetState, double(1),
bips = bips[sort(rownames(bips)), , drop = FALSE])
})
}
<bytecode: 0x558bf54010f8>
<environment: namespace:Quartet>
--- function search by body ---
Function QuartetStates in namespace Quartet has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
NewickParser.cpp:20:63: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
Flavor: r-devel-linux-x86_64-fedora-clang