Last updated on 2019-12-21 10:47:49 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.1 | 17.38 | 189.77 | 207.15 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 3.1 | 13.81 | 139.09 | 152.90 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.1 | 229.47 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.1 | 232.45 | OK | |||
| r-devel-windows-ix86+x86_64 | 3.1 | 41.00 | 259.00 | 300.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 3.1 | 43.00 | 221.00 | 264.00 | OK | |
| r-patched-linux-x86_64 | 3.1 | OK | ||||
| r-patched-solaris-x86 | 3.1 | 317.90 | OK | |||
| r-release-linux-x86_64 | 3.1 | 13.40 | 157.61 | 171.01 | OK | |
| r-release-windows-ix86+x86_64 | 3.1 | 39.00 | 254.00 | 293.00 | OK | |
| r-release-osx-x86_64 | 3.1 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 3.1 | 18.00 | 269.00 | 287.00 | OK | |
| r-oldrel-osx-x86_64 | 3.1 | OK |
Version: 3.1
Check: tests
Result: ERROR
Running 'test-all.R' [71s/77s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
> library(testthat)
> test_check("letsR")
Loading required package: letsR
Loading required package: raster
Loading required package: sp
Loading required package: maps
-- 1. Failure: Other parameters work (@test-TimLucas.r#76) --------------------
class(PresAbMat4) not equal to "matrix".
Lengths differ: 2 is not 1
-- 2. Failure: lets.addpoly works fine, onlyvar = FALSE (@test-lets_addpoly.R#11
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 3. Failure: lets.addpoly works fine, onlyvar = TRUE (@test-lets_addpoly.R#18)
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
-- 4. Failure: lets.addvar works fine (@test-lets_addvar.R#11) ----------------
class(PAM_temp_mean) == "matrix" isn't true.
-- 5. Failure: lets.addvar works fine, different fun (@test-lets_addvar.R#20) -
class(PAM_temp_mean) == "matrix" isn't true.
-- 6. Failure: lets.addvar works fine, onlyvar = TRUE (@test-lets_addvar.R#29)
class(PAM_temp_mean) == "matrix" isn't true.
-- 7. Failure: lets.addvar works fine, multiple rasters (@test-lets_addvar.R#38)
class(PAM_temp_mean) == "matrix" isn't true.
-- 8. Failure: lets.addpoly lets.classvar fine (@test-lets_classvar.R#13) -----
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 9. Failure: lets.addpoly lets.classvar fine, xy = FALSE (@test-lets_classvar.
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 10. Failure: lets.addpoly lets.classvar fine, set groups (@test-lets_classvar
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.distmat(PAM[[1]][1:N, 1:2])
--- call from argument ---
if (class(xy) == "PresenceAbsence") {
xy <- xy[[1]][, 1:2]
}
--- R stacktrace ---
where 1 at testthat/test-lets_correl.R#5: lets.distmat(PAM[[1]][1:N, 1:2])
where 2: eval(code, test_env)
where 3: eval(code, test_env)
where 4: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 10: tryCatchList(expr, classes, parentenv, handlers)
where 11: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 12: test_code(NULL, exprs, env)
where 13: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 14: force(code)
where 15: doWithOneRestart(return(expr), restart)
where 16: withOneRestart(expr, restarts[[1L]])
where 17: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 18: 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 19: FUN(X[[i]], ...)
where 20: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 21: force(code)
where 22: doWithOneRestart(return(expr), restart)
where 23: withOneRestart(expr, restarts[[1L]])
where 24: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 25: 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 26: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 27: 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 28: 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 29: test_check("letsR")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (xy, asdist = TRUE, ...)
{
if (class(xy) == "PresenceAbsence") {
xy <- xy[[1]][, 1:2]
}
if (exists("miles")) {
distan <- rdist.earth(xy, miles = FALSE, ...)
}
else {
distan <- rdist.earth(xy, ...)
}
diag(distan) <- 0
if (asdist) {
distan <- as.dist(distan)
}
return(distan)
}
<bytecode: 0x84f8038>
<environment: namespace:letsR>
--- function search by body ---
Function lets.distmat in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
-- 11. Error: (unknown) (@test-lets_correl.R#5) -------------------------------
the condition has length > 1
Backtrace:
1. letsR::lets.distmat(PAM[[1]][1:N, 1:2])
-- 12. Failure: lets.distmat works fine, asdist = FALSE (@test-lets_distmat.R#22
class(distPAM) == "matrix" isn't true.
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.distmat(coords, miles = TRUE)
--- call from argument ---
if (class(xy) == "PresenceAbsence") {
xy <- xy[[1]][, 1:2]
}
--- R stacktrace ---
where 1 at testthat/test-lets_distmat.R#40: lets.distmat(coords, miles = TRUE)
where 2: eval(code, test_env)
where 3: eval(code, test_env)
where 4: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 10: tryCatchList(expr, classes, parentenv, handlers)
where 11: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 12: test_code(desc, code, env = parent.frame())
where 13 at testthat/test-lets_distmat.R#37: test_that("lets.distmat works fine, xy as matrix ", {
distPAM <- lets.distmat(coords, miles = TRUE)
expect_true(class(distPAM) == "dist")
expect_true(all(dim(as.matrix(distPAM)) == nrow(coords)))
})
where 14: eval(code, test_env)
where 15: eval(code, test_env)
where 16: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 22: tryCatchList(expr, classes, parentenv, handlers)
where 23: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 24: test_code(NULL, exprs, env)
where 25: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 26: force(code)
where 27: doWithOneRestart(return(expr), restart)
where 28: withOneRestart(expr, restarts[[1L]])
where 29: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 30: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 31: FUN(X[[i]], ...)
where 32: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 33: force(code)
where 34: doWithOneRestart(return(expr), restart)
where 35: withOneRestart(expr, restarts[[1L]])
where 36: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 37: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 38: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 39: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 40: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 41: test_check("letsR")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (xy, asdist = TRUE, ...)
{
if (class(xy) == "PresenceAbsence") {
xy <- xy[[1]][, 1:2]
}
if (exists("miles")) {
distan <- rdist.earth(xy, miles = FALSE, ...)
}
else {
distan <- rdist.earth(xy, ...)
}
diag(distan) <- 0
if (asdist) {
distan <- as.dist(distan)
}
return(distan)
}
<bytecode: 0x84f8038>
<environment: namespace:letsR>
--- function search by body ---
Function lets.distmat in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
-- 13. Error: lets.distmat works fine, xy as matrix (@test-lets_distmat.R#40)
the condition has length > 1
Backtrace:
1. letsR::lets.distmat(coords, miles = TRUE)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.field(PAM[[1]], range, PAM$S, xy = TRUE)
--- call from argument ---
if (class(x) == "PresenceAbsence") {
p <- x[[1]][, -(1:2)]
namesSpe <- x[[3]]
}
--- R stacktrace ---
where 1 at testthat/test-lets_field.R#39: lets.field(PAM[[1]], range, PAM$S, xy = TRUE)
where 2: eval(code, test_env)
where 3: eval(code, test_env)
where 4: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 10: tryCatchList(expr, classes, parentenv, handlers)
where 11: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 12: test_code(desc, code, env = parent.frame())
where 13 at testthat/test-lets_field.R#36: test_that("lets.field works fine, matrix and xy = TRUE", {
field <- lets.field(PAM[[1]], range, PAM$S, xy = TRUE)
expect_equal(class(field), "data.frame")
expect_true(ncol(field) == 2)
expect_true(nrow(field) == length(PAM$S))
})
where 14: eval(code, test_env)
where 15: eval(code, test_env)
where 16: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 22: tryCatchList(expr, classes, parentenv, handlers)
where 23: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 24: test_code(NULL, exprs, env)
where 25: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 26: force(code)
where 27: doWithOneRestart(return(expr), restart)
where 28: withOneRestart(expr, restarts[[1L]])
where 29: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 30: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 31: FUN(X[[i]], ...)
where 32: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 33: force(code)
where 34: doWithOneRestart(return(expr), restart)
where 35: withOneRestart(expr, restarts[[1L]])
where 36: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 37: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 38: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 39: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 40: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 41: test_check("letsR")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x, y, z, weight = TRUE, xy = NULL, count = FALSE)
{
if (class(x) == "PresenceAbsence") {
p <- x[[1]][, -(1:2)]
namesSpe <- x[[3]]
}
if (is.matrix(x)) {
if (is.null(xy)) {
stop(paste("Please set if your matrix contains ",
"coordinates in the first two columns", "(xy argument)."),
sep = "")
}
if (xy) {
x <- x[, -(1:2)]
}
p <- x
namesSpe <- colnames(x)
}
if (is.factor(y)) {
y <- as.numeric(levels(y))[y]
}
p2 <- p
for (i in 1:ncol(p2)) {
pos <- z == namesSpe[i]
if (length(pos) > 0) {
p2[, i] <- p2[, i] * y[pos]
pos2 <- p2[, i] == 0
p2[pos2, i] <- NA
}
else {
p2[, i] <- NA
}
}
media <- numeric(ncol(p))
n <- length(media)
if (count) {
if (!"tools:rstudio" %in% search()) {
dev.new(width = 2, height = 2, pointsize = 12)
par(mar = c(0, 0, 0, 0))
}
for (i in 1:n) {
plot.new()
text(0.5, 0.5, paste(paste("Total:", n, "\n", "Runs to go: ",
(n - i))))
media[i] <- .InsiLoop(i, p, p2, weight)
}
dev.off()
}
if (!count) {
for (i in 1:n) {
media[i] <- .InsiLoop(i, p, p2, weight)
}
}
resultado <- cbind(namesSpe, media)
colnames(resultado) <- c("Species", "Value")
resultado <- as.data.frame(resultado)
resultado[, 2] <- as.numeric(levels(resultado[, 2]))[resultado[,
2]]
return(resultado)
}
<bytecode: 0x84fa460>
<environment: namespace:letsR>
--- function search by body ---
Function lets.field in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
-- 14. Error: lets.field works fine, matrix and xy = TRUE (@test-lets_field.R#39
the condition has length > 1
Backtrace:
1. letsR::lets.field(PAM[[1]], range, PAM$S, xy = TRUE)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.field(PAM[[1]][, -(1:2)], range, PAM$S, xy = FALSE)
--- call from argument ---
if (class(x) == "PresenceAbsence") {
p <- x[[1]][, -(1:2)]
namesSpe <- x[[3]]
}
--- R stacktrace ---
where 1 at testthat/test-lets_field.R#50: lets.field(PAM[[1]][, -(1:2)], range, PAM$S, xy = FALSE)
where 2: eval(code, test_env)
where 3: eval(code, test_env)
where 4: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 10: tryCatchList(expr, classes, parentenv, handlers)
where 11: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 12: test_code(desc, code, env = parent.frame())
where 13 at testthat/test-lets_field.R#47: test_that("lets.field works fine, matrix and xy = FALSE", {
field <- lets.field(PAM[[1]][, -(1:2)], range, PAM$S, xy = FALSE)
expect_equal(class(field), "data.frame")
expect_true(ncol(field) == 2)
expect_true(nrow(field) == length(PAM$S))
})
where 14: eval(code, test_env)
where 15: eval(code, test_env)
where 16: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 22: tryCatchList(expr, classes, parentenv, handlers)
where 23: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 24: test_code(NULL, exprs, env)
where 25: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 26: force(code)
where 27: doWithOneRestart(return(expr), restart)
where 28: withOneRestart(expr, restarts[[1L]])
where 29: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 30: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 31: FUN(X[[i]], ...)
where 32: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 33: force(code)
where 34: doWithOneRestart(return(expr), restart)
where 35: withOneRestart(expr, restarts[[1L]])
where 36: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 37: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 38: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 39: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 40: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 41: test_check("letsR")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x, y, z, weight = TRUE, xy = NULL, count = FALSE)
{
if (class(x) == "PresenceAbsence") {
p <- x[[1]][, -(1:2)]
namesSpe <- x[[3]]
}
if (is.matrix(x)) {
if (is.null(xy)) {
stop(paste("Please set if your matrix contains ",
"coordinates in the first two columns", "(xy argument)."),
sep = "")
}
if (xy) {
x <- x[, -(1:2)]
}
p <- x
namesSpe <- colnames(x)
}
if (is.factor(y)) {
y <- as.numeric(levels(y))[y]
}
p2 <- p
for (i in 1:ncol(p2)) {
pos <- z == namesSpe[i]
if (length(pos) > 0) {
p2[, i] <- p2[, i] * y[pos]
pos2 <- p2[, i] == 0
p2[pos2, i] <- NA
}
else {
p2[, i] <- NA
}
}
media <- numeric(ncol(p))
n <- length(media)
if (count) {
if (!"tools:rstudio" %in% search()) {
dev.new(width = 2, height = 2, pointsize = 12)
par(mar = c(0, 0, 0, 0))
}
for (i in 1:n) {
plot.new()
text(0.5, 0.5, paste(paste("Total:", n, "\n", "Runs to go: ",
(n - i))))
media[i] <- .InsiLoop(i, p, p2, weight)
}
dev.off()
}
if (!count) {
for (i in 1:n) {
media[i] <- .InsiLoop(i, p, p2, weight)
}
}
resultado <- cbind(namesSpe, media)
colnames(resultado) <- c("Species", "Value")
resultado <- as.data.frame(resultado)
resultado[, 2] <- as.numeric(levels(resultado[, 2]))[resultado[,
2]]
return(resultado)
}
<bytecode: 0x84fa460>
<environment: namespace:letsR>
--- function search by body ---
Function lets.field in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
-- 15. Error: lets.field works fine, matrix and xy = FALSE (@test-lets_field.R#5
the condition has length > 1
Backtrace:
1. letsR::lets.field(PAM[[1]][, -(1:2)], range, PAM$S, xy = FALSE)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.field(PAM[[1]], range, PAM$S)
--- call from argument ---
if (class(x) == "PresenceAbsence") {
p <- x[[1]][, -(1:2)]
namesSpe <- x[[3]]
}
--- R stacktrace ---
where 1: lets.field(PAM[[1]], range, PAM$S)
where 2: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
where 3: withCallingHandlers({
code
NULL
}, error = function(cnd) {
if (can_entrace(cnd)) {
cnd <- cnd_entrace(cnd)
}
return_from(env, cnd)
})
where 4: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),
...)
where 5: quasi_capture(enquo(object), label, capture_error, entrace = TRUE)
where 6 at testthat/test-lets_field.R#60: expect_error(lets.field(PAM[[1]], range, PAM$S))
where 7: eval(code, test_env)
where 8: eval(code, test_env)
where 9: 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 10: doTryCatch(return(expr), name, parentenv, handler)
where 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 13: doTryCatch(return(expr), name, parentenv, handler)
where 14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 15: tryCatchList(expr, classes, parentenv, handlers)
where 16: 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 17: test_code(desc, code, env = parent.frame())
where 18 at testthat/test-lets_field.R#57: test_that("lets.field error expected, matrix without xy", {
expect_error(lets.field(PAM[[1]], range, PAM$S))
})
where 19: eval(code, test_env)
where 20: eval(code, test_env)
where 21: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 25: doTryCatch(return(expr), name, parentenv, handler)
where 26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 27: tryCatchList(expr, classes, parentenv, handlers)
where 28: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 29: test_code(NULL, exprs, env)
where 30: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 31: force(code)
where 32: doWithOneRestart(return(expr), restart)
where 33: withOneRestart(expr, restarts[[1L]])
where 34: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 35: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$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 36: FUN(X[[i]], ...)
where 37: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 38: force(code)
where 39: doWithOneRestart(return(expr), restart)
where 40: withOneRestart(expr, restarts[[1L]])
where 41: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 42: 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 43: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: 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 45: 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 46: test_check("letsR")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x, y, z, weight = TRUE, xy = NULL, count = FALSE)
{
if (class(x) == "PresenceAbsence") {
p <- x[[1]][, -(1:2)]
namesSpe <- x[[3]]
}
if (is.matrix(x)) {
if (is.null(xy)) {
stop(paste("Please set if your matrix contains ",
"coordinates in the first two columns", "(xy argument)."),
sep = "")
}
if (xy) {
x <- x[, -(1:2)]
}
p <- x
namesSpe <- colnames(x)
}
if (is.factor(y)) {
y <- as.numeric(levels(y))[y]
}
p2 <- p
for (i in 1:ncol(p2)) {
pos <- z == namesSpe[i]
if (length(pos) > 0) {
p2[, i] <- p2[, i] * y[pos]
pos2 <- p2[, i] == 0
p2[pos2, i] <- NA
}
else {
p2[, i] <- NA
}
}
media <- numeric(ncol(p))
n <- length(media)
if (count) {
if (!"tools:rstudio" %in% search()) {
dev.new(width = 2, height = 2, pointsize = 12)
par(mar = c(0, 0, 0, 0))
}
for (i in 1:n) {
plot.new()
text(0.5, 0.5, paste(paste("Total:", n, "\n", "Runs to go: ",
(n - i))))
media[i] <- .InsiLoop(i, p, p2, weight)
}
dev.off()
}
if (!count) {
for (i in 1:n) {
media[i] <- .InsiLoop(i, p, p2, weight)
}
}
resultado <- cbind(namesSpe, media)
colnames(resultado) <- c("Species", "Value")
resultado <- as.data.frame(resultado)
resultado[, 2] <- as.numeric(levels(resultado[, 2]))[resultado[,
2]]
return(resultado)
}
<bytecode: 0x84fa460>
<environment: namespace:letsR>
--- function search by body ---
Function lets.field in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
-- 16. Failure: lets.gridirizer works fine (@test-lets_gridirizer.R#11) -------
class(resu_test[[2]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 17. Failure: lets.maplizer works fine (@test-lets_maplizer.R#10) -----------
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 18. Failure: lets.maplizer works fine, other func (@test-lets_maplizer.R#17)
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 19. Failure: lets.maplizer works fine (@test-lets_maplizer.R#25) -----------
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.distmat(pam2[loc, 1:2], asdist = FALSE)
--- call from argument ---
if (class(xy) == "PresenceAbsence") {
xy <- xy[[1]][, 1:2]
}
--- R stacktrace ---
where 1: lets.distmat(pam2[loc, 1:2], asdist = FALSE)
where 2 at testthat/test-lets_midpoint.R#40: lets.midpoint(PAM, method = "CMD")
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: 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 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: 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 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-lets_midpoint.R#37: test_that("lets.midpoint works fine, method = CMD", {
resu_test <- lets.midpoint(PAM, method = "CMD")
expect_equal(class(resu_test), "data.frame")
expect_true(ncol(resu_test) == 3)
expect_true(!any(is.na(resu_test)))
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: 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 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: 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 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: 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 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: 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 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: 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 41: 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 42: test_check("letsR")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (xy, asdist = TRUE, ...)
{
if (class(xy) == "PresenceAbsence") {
xy <- xy[[1]][, 1:2]
}
if (exists("miles")) {
distan <- rdist.earth(xy, miles = FALSE, ...)
}
else {
distan <- rdist.earth(xy, ...)
}
diag(distan) <- 0
if (asdist) {
distan <- as.dist(distan)
}
return(distan)
}
<bytecode: 0x84f8038>
<environment: namespace:letsR>
--- function search by body ---
Function lets.distmat in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
-- 20. Error: lets.midpoint works fine, method = CMD (@test-lets_midpoint.R#40)
the condition has length > 1
Backtrace:
1. letsR::lets.midpoint(PAM, method = "CMD")
2. letsR::lets.distmat(pam2[loc, 1:2], asdist = FALSE)
-- 21. Failure: lets.overlap works fine, Chesser&Zink (@test-lets_overlap.R#11)
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.overlap(PAM[[1]][, -c(1, 2)], method = "Chesser&Zink", xy = FALSE)
--- call from argument ---
if (class(pam) == "PresenceAbsence") {
pam <- pam[[1]][, -(1:2), drop = FALSE]
}
--- R stacktrace ---
where 1 at testthat/test-lets_overlap.R#20: lets.overlap(PAM[[1]][, -c(1, 2)], method = "Chesser&Zink", xy = FALSE)
where 2: eval(code, test_env)
where 3: eval(code, test_env)
where 4: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 10: tryCatchList(expr, classes, parentenv, handlers)
where 11: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 12: test_code(desc, code, env = parent.frame())
where 13 at testthat/test-lets_overlap.R#17: test_that("lets.overlap works fine, xy = FALSE", {
resu_test <- lets.overlap(PAM[[1]][, -c(1, 2)], method = "Chesser&Zink",
xy = FALSE)
expect_equal(class(resu_test), "matrix")
expect_true(all(dim(resu_test) == length(PAM[[3]])))
expect_true(!any(is.na(resu_test)))
})
where 14: eval(code, test_env)
where 15: eval(code, test_env)
where 16: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 22: tryCatchList(expr, classes, parentenv, handlers)
where 23: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 24: test_code(NULL, exprs, env)
where 25: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 26: force(code)
where 27: doWithOneRestart(return(expr), restart)
where 28: withOneRestart(expr, restarts[[1L]])
where 29: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 30: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 31: FUN(X[[i]], ...)
where 32: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 33: force(code)
where 34: doWithOneRestart(return(expr), restart)
where 35: withOneRestart(expr, restarts[[1L]])
where 36: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 37: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 38: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 39: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 40: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 41: test_check("letsR")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (pam, method = "Chesser&Zink", xy = NULL)
{
methods <- c("Chesser&Zink", "Proportional", "Cells")
if (!any(method == methods)) {
stop(paste("The method", method, "is not implemented.",
"Please check the spelling."))
}
if (!any(class(pam) %in% c("matrix", "PresenceAbsence"))) {
stop(paste("Object pam should be either a PresenceAbsence or a matrix.\n Not a",
class(pam)))
}
if (is.matrix(pam)) {
if (is.null(xy)) {
stop(paste("Please set if your matrix contains ",
"coordinates in the first two columns", "(xy argument)."),
sep = "")
}
if (xy) {
pam <- pam[, -(1:2), drop = FALSE]
}
}
if (class(pam) == "PresenceAbsence") {
pam <- pam[[1]][, -(1:2), drop = FALSE]
}
nomes <- colnames(pam)
n <- ncol(pam)
resu <- matrix(NA, ncol = n, nrow = n)
if (method == "Cells") {
diag(resu) <- 1
for (i in 1:(n - 1)) {
for (j in ((i + 1):n)) {
over <- sum(rowSums(pam[, c(i, j)]) == 2)
resu[i, j] <- over
}
}
ind <- lower.tri(resu)
resu[ind] <- t(resu)[ind]
}
if (method == "Proportional") {
range <- colSums(pam)
for (i in 1:n) {
for (j in 1:n) {
over <- sum(rowSums(pam[, c(i, j)]) == 2)
if (range[i] == 0) {
over2 <- 0
}
else {
over2 <- over/range[i]
}
resu[i, j] <- over2
}
}
}
if (method == "Chesser&Zink") {
range <- colSums(pam)
diag(resu) <- 1
for (i in 1:(n - 1)) {
for (j in ((i + 1):n)) {
over <- sum(rowSums(pam[, c(i, j)]) == 2)
if (any(range[c(i, j)] %in% 0)) {
resu[i, j] <- 0
}
else {
resu[i, j] <- over/min(range[c(i, j)])
}
}
}
ind <- lower.tri(resu)
resu[ind] <- t(resu)[ind]
}
colnames(resu) <- nomes
rownames(resu) <- nomes
return(resu)
}
<bytecode: 0x84c9058>
<environment: namespace:letsR>
--- function search by body ---
Function lets.overlap in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
-- 22. Error: lets.overlap works fine, xy = FALSE (@test-lets_overlap.R#20) ---
the condition has length > 1
Backtrace:
1. letsR::lets.overlap(...)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.overlap(PAM[[1]], method = "Chesser&Zink", xy = TRUE)
--- call from argument ---
if (class(pam) == "PresenceAbsence") {
pam <- pam[[1]][, -(1:2), drop = FALSE]
}
--- R stacktrace ---
where 1 at testthat/test-lets_overlap.R#33: lets.overlap(PAM[[1]], method = "Chesser&Zink", xy = TRUE)
where 2: eval(code, test_env)
where 3: eval(code, test_env)
where 4: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 10: tryCatchList(expr, classes, parentenv, handlers)
where 11: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 12: test_code(desc, code, env = parent.frame())
where 13 at testthat/test-lets_overlap.R#30: test_that("lets.overlap works fine, xy = TRUE", {
resu_test <- lets.overlap(PAM[[1]], method = "Chesser&Zink",
xy = TRUE)
expect_equal(class(resu_test), "matrix")
expect_true(all(dim(resu_test) == length(PAM[[3]])))
expect_true(!any(is.na(resu_test)))
})
where 14: eval(code, test_env)
where 15: eval(code, test_env)
where 16: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 22: tryCatchList(expr, classes, parentenv, handlers)
where 23: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 24: test_code(NULL, exprs, env)
where 25: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 26: force(code)
where 27: doWithOneRestart(return(expr), restart)
where 28: withOneRestart(expr, restarts[[1L]])
where 29: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 30: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 31: FUN(X[[i]], ...)
where 32: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 33: force(code)
where 34: doWithOneRestart(return(expr), restart)
where 35: withOneRestart(expr, restarts[[1L]])
where 36: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 37: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 38: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 39: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 40: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 41: test_check("letsR")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (pam, method = "Chesser&Zink", xy = NULL)
{
methods <- c("Chesser&Zink", "Proportional", "Cells")
if (!any(method == methods)) {
stop(paste("The method", method, "is not implemented.",
"Please check the spelling."))
}
if (!any(class(pam) %in% c("matrix", "PresenceAbsence"))) {
stop(paste("Object pam should be either a PresenceAbsence or a matrix.\n Not a",
class(pam)))
}
if (is.matrix(pam)) {
if (is.null(xy)) {
stop(paste("Please set if your matrix contains ",
"coordinates in the first two columns", "(xy argument)."),
sep = "")
}
if (xy) {
pam <- pam[, -(1:2), drop = FALSE]
}
}
if (class(pam) == "PresenceAbsence") {
pam <- pam[[1]][, -(1:2), drop = FALSE]
}
nomes <- colnames(pam)
n <- ncol(pam)
resu <- matrix(NA, ncol = n, nrow = n)
if (method == "Cells") {
diag(resu) <- 1
for (i in 1:(n - 1)) {
for (j in ((i + 1):n)) {
over <- sum(rowSums(pam[, c(i, j)]) == 2)
resu[i, j] <- over
}
}
ind <- lower.tri(resu)
resu[ind] <- t(resu)[ind]
}
if (method == "Proportional") {
range <- colSums(pam)
for (i in 1:n) {
for (j in 1:n) {
over <- sum(rowSums(pam[, c(i, j)]) == 2)
if (range[i] == 0) {
over2 <- 0
}
else {
over2 <- over/range[i]
}
resu[i, j] <- over2
}
}
}
if (method == "Chesser&Zink") {
range <- colSums(pam)
diag(resu) <- 1
for (i in 1:(n - 1)) {
for (j in ((i + 1):n)) {
over <- sum(rowSums(pam[, c(i, j)]) == 2)
if (any(range[c(i, j)] %in% 0)) {
resu[i, j] <- 0
}
else {
resu[i, j] <- over/min(range[c(i, j)])
}
}
}
ind <- lower.tri(resu)
resu[ind] <- t(resu)[ind]
}
colnames(resu) <- nomes
rownames(resu) <- nomes
return(resu)
}
<bytecode: 0x84c9058>
<environment: namespace:letsR>
--- function search by body ---
Function lets.overlap in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
-- 23. Error: lets.overlap works fine, xy = TRUE (@test-lets_overlap.R#33) ----
the condition has length > 1
Backtrace:
1. letsR::lets.overlap(PAM[[1]], method = "Chesser&Zink", xy = TRUE)
-- 24. Failure: lets.overlap works fine, Cells (@test-lets_overlap.R#47) ------
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 25. Failure: lets.overlap works fine, Proportional (@test-lets_overlap.R#57)
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 26. Failure: lets.pamcrop works fine, remove.sp = TRUE (@test-lets_pamcrop.R#
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 27. Failure: lets.pamcrop works fine, remove.sp = FALSE (@test-lets_pamcrop.R
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 28. Failure: lets.presab.birds return a correct PresenceAbsence object (@test
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 29. Failure: lets.presab.grid works fine (@test-lets_presab_grid.R#16) -----
class(resu[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 30. Failure: lets.presab.points return a correct PresenceAbsence object (@tes
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 31. Failure: lets.presab.points return a correct PresenceAbsence object for t
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 32. Failure: lets.presab.points return a correct PresenceAbsence object (coun
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 33. Failure: lets.presab.points return a correct PresenceAbsence object, remo
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 34. Failure: lets.presab.points return a correct PresenceAbsence object, remo
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 35. Failure: lets.rangesize works fine, geographic (@test-lets_rangesize.R#13
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 36. Failure: lets.rangesize works fine, planar (@test-lets_rangesize.R#25) -
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 37. Failure: lets.rangesize works fine, squaremeter (@test-lets_rangesize.R#3
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 38. Failure: lets.rangesize works fine, squaremeter (@test-lets_rangesize.R#4
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 39. Failure: lets.rangesize works fine, squaremeter global (@test-lets_ranges
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
-- 40. Failure: lets.subsetPAM works fine, remove.cells = TRUE (@test-lets_subse
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
-- 41. Failure: lets.subsetPAM works fine, remove.cells = FALSE (@test-lets_subs
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.subsetPAM(PAM[[1]], PAM[[3]][1:20])
--- call from argument ---
if (class(x) != "PresenceAbsence") {
stop("x argument must be a PresenceAbsence object")
}
--- R stacktrace ---
where 1: lets.subsetPAM(PAM[[1]], PAM[[3]][1:20])
where 2: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
where 3: withCallingHandlers({
code
NULL
}, error = function(cnd) {
if (can_entrace(cnd)) {
cnd <- cnd_entrace(cnd)
}
return_from(env, cnd)
})
where 4: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),
...)
where 5: quasi_capture(enquo(object), label, capture_error, entrace = TRUE)
where 6 at testthat/test-lets_subsetPAM.R#39: expect_error(lets.subsetPAM(PAM[[1]], PAM[[3]][1:20]))
where 7: eval(code, test_env)
where 8: eval(code, test_env)
where 9: 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 10: doTryCatch(return(expr), name, parentenv, handler)
where 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 13: doTryCatch(return(expr), name, parentenv, handler)
where 14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 15: tryCatchList(expr, classes, parentenv, handlers)
where 16: 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 17: test_code(desc, code, env = parent.frame())
where 18 at testthat/test-lets_subsetPAM.R#36: test_that("lets.subsetPAM error check", {
expect_error(lets.subsetPAM(PAM, "Bruno"))
expect_error(lets.subsetPAM(PAM[[1]], PAM[[3]][1:20]))
expect_error(lets.subsetPAM(PAM, 1))
expect_error(lets.subsetPAM(PAM[[1]], PAM[[3]][1:20]))
expect_error(lets.subsetPAM(PAM, PAM[[3]][1:20], 1))
expect_warning(lets.subsetPAM(PAM, c("Bruno", PAM[[3]][1:20])))
})
where 19: eval(code, test_env)
where 20: eval(code, test_env)
where 21: 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 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 25: doTryCatch(return(expr), name, parentenv, handler)
where 26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 27: tryCatchList(expr, classes, parentenv, handlers)
where 28: 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 29: test_code(NULL, exprs, env)
where 30: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 31: force(code)
where 32: doWithOneRestart(return(expr), restart)
where 33: withOneRestart(expr, restarts[[1L]])
where 34: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 35: 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 36: FUN(X[[i]], ...)
where 37: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 38: force(code)
where 39: doWithOneRestart(return(expr), restart)
where 40: withOneRestart(expr, restarts[[1L]])
where 41: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 42: 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 43: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: 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 45: 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 46: test_check("letsR")
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (x, names, remove.cells = TRUE)
{
if (class(x) != "PresenceAbsence") {
stop("x argument must be a PresenceAbsence object")
}
if (class(names) != "character") {
stop("names argument must be a character object")
}
if (class(remove.cells) != "logical") {
stop("remove.cells argument must be a TRUE or FALSE")
}
pos <- colnames(x[[1]]) %in% names
errorcont <- names %in% colnames(x[[1]])
if (!any(errorcont)) {
stop("None of the names provided match with PAM species")
}
if (any(!errorcont)) {
warning(paste("One or more names", "provided, do not",
"match any of the", "PAM species"))
}
x[[1]] <- x[[1]][, c(1:2, which(pos)), drop = FALSE]
if (remove.cells) {
x[[1]] <- .removeCells(x[[1]])
}
rich <- rowSums(x[[1]][, -(1:2), drop = FALSE])
x[[2]] <- rasterize(x[[1]][, c(1:2), drop = FALSE], x[[2]],
rich)
x[[3]] <- colnames(x[[1]])[-c(1:2)]
return(x)
}
<bytecode: 0x84a6df8>
<environment: namespace:letsR>
--- function search by body ---
Function lets.subsetPAM in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
letsR
--- call from context ---
lets.subsetPAM(PAM[[1]], PAM[[3]][1:20])
--- call from argument ---
if (class(x) != "PresenceAbsence") {
stop("x argument must be a PresenceAbsence object")
}
--- R stacktrace ---
where 1: lets.subsetPAM(PAM[[1]], PAM[[3]][1:20])
where 2: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
where 3: withCallingHandlers({
code
NULL
}, error = function(cnd) {
if (can_entrace(cnd)) {
cnd <- cnd_entrace(cnd)
}
return_from(env, cnd)
})
where 4: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),
...)
where 5: quasi_capture(enquo(object), label, capture_error, entrace = TRUE)
where 6 at testthat/test-lets_subsetPAM.R#41: expect_error(lets.subsetPAM(PAM[[1]], PAM[[3]][1:20]))
where 7: eval(code, test_env)
where 8: eval(code, test_env)
where 9: 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 10: doTryCatch(return(expr), name, parentenv, handler)
where 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 13: doTryCatch(return(expr), name, parentenv, handler)
where 14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 15: tryCatchList(expr, classes, parentenv, handlers)
where 16: 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 17: test_code(desc, code, env = parent.frame())
where 18 at testthat/test-lets_subsetPAM.R#36: test_that("lets.subsetPAM error check", {
expect_error(lets.subsetPAM(PAM, "Bruno"))
expect_error(lets.subsetPAM(PAM[[1]], PAM[[3]][1:20]))
expect_error(lets.subsetPAM(PAM, 1))
expect_error(lets.subsetPAM(PAM[[1]], PAM[[3]][1:20]))
expect_error(lets.subsetPAM(PAM, PAM[[3]][1:20], 1))
expect_warning(lets.subsetPAM(PAM, c("Bruno", PAM[[3]][1:20])))
})
where 19: eval(code, test_env)
where 20: eval(code, test_env)
where 21: 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 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 25: doTryCatch(return(expr), name, parentenv, handler)
where 26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 27: tryCatchList(expr, classes, parentenv, handlers)
where 28: 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 29: test_code(NULL, exprs, env)
where 30: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 31: force(code)
where 32: doWithOneRestart(return(expr), restart)
where 33: withOneRestart(expr, restarts[[1L]])
where 34: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 35: 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 36: FUN(X[[i]], ...)
where 37: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 38: force(code)
where 39: doWithOneRestart(return(expr), restart)
where 40: withOneRestart(expr, restarts[[1L]])
where 41: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 42: 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 43: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: 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 45: 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 46: test_check("letsR")
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (x, names, remove.cells = TRUE)
{
if (class(x) != "PresenceAbsence") {
stop("x argument must be a PresenceAbsence object")
}
if (class(names) != "character") {
stop("names argument must be a character object")
}
if (class(remove.cells) != "logical") {
stop("remove.cells argument must be a TRUE or FALSE")
}
pos <- colnames(x[[1]]) %in% names
errorcont <- names %in% colnames(x[[1]])
if (!any(errorcont)) {
stop("None of the names provided match with PAM species")
}
if (any(!errorcont)) {
warning(paste("One or more names", "provided, do not",
"match any of the", "PAM species"))
}
x[[1]] <- x[[1]][, c(1:2, which(pos)), drop = FALSE]
if (remove.cells) {
x[[1]] <- .removeCells(x[[1]])
}
rich <- rowSums(x[[1]][, -(1:2), drop = FALSE])
x[[2]] <- rasterize(x[[1]][, c(1:2), drop = FALSE], x[[2]],
rich)
x[[3]] <- colnames(x[[1]])[-c(1:2)]
return(x)
}
<bytecode: 0x84a6df8>
<environment: namespace:letsR>
--- function search by body ---
Function lets.subsetPAM in namespace letsR has this body.
----------- END OF FAILURE REPORT --------------
Class: PresenceAbsence
Number of species: 32
Number of cells: 1168
Resolution: 1, 1 (x, y)
Class: PresenceAbsence
_ _
Number of species: 32
Number of cells: 1168
Cells with presence: 1168
Cells without presence: 0
Species without presence: 0
Species with the largest range: Phyllomedusa hypochondrialis
_ _
Grid parameters
Resolution: 1, 1 (x, y)
Extention: -93, -29, -57, 15 (xmin, xmax, ymin, ymax)
Coord. Ref.: +proj=longlat +datum=WGS84== testthat results ===========================================================
[ OK: 138 | SKIPPED: 15 | WARNINGS: 11 | FAILED: 41 ]
1. Failure: Other parameters work (@test-TimLucas.r#76)
2. Failure: lets.addpoly works fine, onlyvar = FALSE (@test-lets_addpoly.R#11)
3. Failure: lets.addpoly works fine, onlyvar = TRUE (@test-lets_addpoly.R#18)
4. Failure: lets.addvar works fine (@test-lets_addvar.R#11)
5. Failure: lets.addvar works fine, different fun (@test-lets_addvar.R#20)
6. Failure: lets.addvar works fine, onlyvar = TRUE (@test-lets_addvar.R#29)
7. Failure: lets.addvar works fine, multiple rasters (@test-lets_addvar.R#38)
8. Failure: lets.addpoly lets.classvar fine (@test-lets_classvar.R#13)
9. Failure: lets.addpoly lets.classvar fine, xy = FALSE (@test-lets_classvar.R#24)
1. ...
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 3.1
Check: tests
Result: ERROR
Running ‘test-all.R’ [48s/68s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("letsR")
Loading required package: letsR
Loading required package: raster
Loading required package: sp
Loading required package: maps
── 1. Failure: Other parameters work (@test-TimLucas.r#76) ────────────────────
class(PresAbMat4) not equal to "matrix".
Lengths differ: 2 is not 1
── 2. Failure: lets.addpoly works fine, onlyvar = FALSE (@test-lets_addpoly.R#11
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 3. Failure: lets.addpoly works fine, onlyvar = TRUE (@test-lets_addpoly.R#18)
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
── 4. Failure: lets.addvar works fine (@test-lets_addvar.R#11) ────────────────
class(PAM_temp_mean) == "matrix" isn't true.
── 5. Failure: lets.addvar works fine, different fun (@test-lets_addvar.R#20) ─
class(PAM_temp_mean) == "matrix" isn't true.
── 6. Failure: lets.addvar works fine, onlyvar = TRUE (@test-lets_addvar.R#29)
class(PAM_temp_mean) == "matrix" isn't true.
── 7. Failure: lets.addvar works fine, multiple rasters (@test-lets_addvar.R#38)
class(PAM_temp_mean) == "matrix" isn't true.
── 8. Failure: lets.addpoly lets.classvar fine (@test-lets_classvar.R#13) ─────
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 9. Failure: lets.addpoly lets.classvar fine, xy = FALSE (@test-lets_classvar.
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 10. Failure: lets.addpoly lets.classvar fine, set groups (@test-lets_classvar
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 11. Failure: lets.correl works fine (@test-lets_correl.R#13) ───────────────
class(correl) == "matrix" isn't true.
── 12. Failure: lets.correl works fine, equidistant = TRUE (@test-lets_correl.R#
class(correl) == "matrix" isn't true.
── 13. Failure: lets.correl works fine, plot = TRUE (@test-lets_correl.R#27) ──
class(correl) == "matrix" isn't true.
── 14. Failure: lets.correl works fine, matrix (@test-lets_correl.R#35) ───────
class(correl) == "matrix" isn't true.
── 15. Failure: lets.correl works fine, multiple (@test-lets_correl.R#42) ─────
class(correl) == "matrix" isn't true.
── 16. Failure: lets.distmat works fine, asdist = FALSE (@test-lets_distmat.R#22
class(distPAM) == "matrix" isn't true.
── 17. Failure: lets.gridirizer works fine (@test-lets_gridirizer.R#11) ───────
class(resu_test[[2]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 18. Failure: lets.maplizer works fine (@test-lets_maplizer.R#10) ───────────
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 19. Failure: lets.maplizer works fine, other func (@test-lets_maplizer.R#17)
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 20. Failure: lets.maplizer works fine (@test-lets_maplizer.R#25) ───────────
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 21. Failure: lets.overlap works fine, Chesser&Zink (@test-lets_overlap.R#11)
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 22. Failure: lets.overlap works fine, xy = FALSE (@test-lets_overlap.R#24) ─
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 23. Failure: lets.overlap works fine, xy = TRUE (@test-lets_overlap.R#37) ──
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 24. Failure: lets.overlap works fine, Cells (@test-lets_overlap.R#47) ──────
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 25. Failure: lets.overlap works fine, Proportional (@test-lets_overlap.R#57)
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 26. Failure: lets.pamcrop works fine, remove.sp = TRUE (@test-lets_pamcrop.R#
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 27. Failure: lets.pamcrop works fine, remove.sp = FALSE (@test-lets_pamcrop.R
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 28. Failure: lets.presab.birds return a correct PresenceAbsence object (@test
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 29. Failure: lets.presab.grid works fine (@test-lets_presab_grid.R#16) ─────
class(resu[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 30. Failure: lets.presab.points return a correct PresenceAbsence object (@tes
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 31. Failure: lets.presab.points return a correct PresenceAbsence object for t
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 32. Failure: lets.presab.points return a correct PresenceAbsence object (coun
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 33. Failure: lets.presab.points return a correct PresenceAbsence object, remo
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 34. Failure: lets.presab.points return a correct PresenceAbsence object, remo
class(PAM[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 35. Failure: lets.rangesize works fine, geographic (@test-lets_rangesize.R#13
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 36. Failure: lets.rangesize works fine, planar (@test-lets_rangesize.R#25) ─
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 37. Failure: lets.rangesize works fine, squaremeter (@test-lets_rangesize.R#3
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 38. Failure: lets.rangesize works fine, squaremeter (@test-lets_rangesize.R#4
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 39. Failure: lets.rangesize works fine, squaremeter global (@test-lets_ranges
class(resu_test) not equal to "matrix".
Lengths differ: 2 is not 1
── 40. Failure: lets.subsetPAM works fine, remove.cells = TRUE (@test-lets_subse
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
── 41. Failure: lets.subsetPAM works fine, remove.cells = FALSE (@test-lets_subs
class(resu_test[[1]]) not equal to "matrix".
Lengths differ: 2 is not 1
Class: PresenceAbsence
Number of species: 32
Number of cells: 1168
Resolution: 1, 1 (x, y)
Class: PresenceAbsence
_ _
Number of species: 32
Number of cells: 1168
Cells with presence: 1168
Cells without presence: 0
Species without presence: 0
Species with the largest range: Phyllomedusa hypochondrialis
_ _
Grid parameters
Resolution: 1, 1 (x, y)
Extention: -93, -29, -57, 15 (xmin, xmax, ymin, ymax)
Coord. Ref.: +proj=longlat +datum=WGS84══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 160 | SKIPPED: 15 | WARNINGS: 48 | FAILED: 41 ]
1. Failure: Other parameters work (@test-TimLucas.r#76)
2. Failure: lets.addpoly works fine, onlyvar = FALSE (@test-lets_addpoly.R#11)
3. Failure: lets.addpoly works fine, onlyvar = TRUE (@test-lets_addpoly.R#18)
4. Failure: lets.addvar works fine (@test-lets_addvar.R#11)
5. Failure: lets.addvar works fine, different fun (@test-lets_addvar.R#20)
6. Failure: lets.addvar works fine, onlyvar = TRUE (@test-lets_addvar.R#29)
7. Failure: lets.addvar works fine, multiple rasters (@test-lets_addvar.R#38)
8. Failure: lets.addpoly lets.classvar fine (@test-lets_classvar.R#13)
9. Failure: lets.addpoly lets.classvar fine, xy = FALSE (@test-lets_classvar.R#24)
1. ...
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc