Last updated on 2019-05-30 11:56:30 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.4 | 25.04 | 203.76 | 228.80 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.4 | 21.99 | 156.28 | 178.27 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.4 | 270.97 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.4 | 272.44 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.2.4 | 56.00 | 288.00 | 344.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.4 | 26.04 | 199.68 | 225.72 | ERROR | |
| r-patched-solaris-x86 | 0.2.4 | 387.70 | ERROR | |||
| r-release-linux-x86_64 | 0.2.4 | 26.00 | 201.19 | 227.19 | ERROR | |
| r-release-windows-ix86+x86_64 | 0.2.4 | 4.00 | 6.00 | 10.00 | ERROR | |
| r-release-osx-x86_64 | 0.2.4 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.2.4 | 50.00 | 272.00 | 322.00 | ERROR | |
| r-oldrel-osx-x86_64 | 0.2.4 | NOTE |
Version: 0.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [38s/42s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(SSDM)
Welcome to the SSDM package, you can launch the graphical user interface by typing gui() in the console.
>
> test_check("SSDM")
-- 1. Error: ensemble function (@test_ensemble.R#7) ---------------------------
subscript out of bounds
1: modelling("SVM", Occurrences, Env, Xcol = "LONGITUDE", Ycol = "LATITUDE", select.thresh = 0,
verbose = FALSE) at testthat/test_ensemble.R:7
2: project(model, Env, ...)
3: project(model, Env, ...)
4: suppressWarnings(raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
}))
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
6: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
7: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
8: .local(object, ...)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
-- 2. Error: ensemble modelling function (@test_ensemble_modelling.R#5) -------
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "MARS"), Occurrences, Env, rep = 1, Xcol = "LONGITUDE",
Ycol = "LATITUDE", ensemble.thresh = c(0), verbose = FALSE) at testthat/test_ensemble_modelling.R:5
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
-- 3. Failure: stack modelling function (@test_stack_modelling.R#8) -----------
`SSDM` inherits from `NULL` not `Stacked.SDM`.
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
-- 4. Error: stacking function (@test_stacking.R#6) ---------------------------
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "SVM"), Occ1, Env, rep = 1, Xcol = "LONGITUDE", Ycol = "LATITUDE",
name = "elliptica", ensemble.thresh = 0, verbose = FALSE) at testthat/test_stacking.R:6
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(name = "elliptica", thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
== testthat results ===========================================================
OK: 43 SKIPPED: 0 WARNINGS: 15 FAILED: 4
1. Error: ensemble function (@test_ensemble.R#7)
2. Error: ensemble modelling function (@test_ensemble_modelling.R#5)
3. Failure: stack modelling function (@test_stack_modelling.R#8)
4. Error: stacking function (@test_stacking.R#6)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'GUI.Rmd' using rmarkdown
--- finished re-building 'GUI.Rmd'
--- re-building 'SSDM.Rmd' using rmarkdown
Quitting from lines 92-96 (SSDM.Rmd)
Error: processing vignette 'SSDM.Rmd' failed with diagnostics:
unable to find an inherited method for function 'ensemble' for signature '"missing"'
--- failed re-building 'SSDM.Rmd'
SUMMARY: processing the following file failed:
'SSDM.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [26s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(SSDM)
Welcome to the SSDM package, you can launch the graphical user interface by typing gui() in the console.
>
> test_check("SSDM")
── 1. Error: ensemble function (@test_ensemble.R#7) ───────────────────────────
subscript out of bounds
1: modelling("SVM", Occurrences, Env, Xcol = "LONGITUDE", Ycol = "LATITUDE", select.thresh = 0,
verbose = FALSE) at testthat/test_ensemble.R:7
2: project(model, Env, ...)
3: project(model, Env, ...)
4: suppressWarnings(raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
}))
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
6: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
7: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
8: .local(object, ...)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 2. Error: ensemble modelling function (@test_ensemble_modelling.R#5) ───────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "MARS"), Occurrences, Env, rep = 1, Xcol = "LONGITUDE",
Ycol = "LATITUDE", ensemble.thresh = c(0), verbose = FALSE) at testthat/test_ensemble_modelling.R:5
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
── 3. Failure: stack modelling function (@test_stack_modelling.R#8) ───────────
`SSDM` inherits from `NULL` not `Stacked.SDM`.
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 4. Error: stacking function (@test_stacking.R#6) ───────────────────────────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "SVM"), Occ1, Env, rep = 1, Xcol = "LONGITUDE", Ycol = "LATITUDE",
name = "elliptica", ensemble.thresh = 0, verbose = FALSE) at testthat/test_stacking.R:6
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(name = "elliptica", thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 43 SKIPPED: 0 WARNINGS: 15 FAILED: 4
1. Error: ensemble function (@test_ensemble.R#7)
2. Error: ensemble modelling function (@test_ensemble_modelling.R#5)
3. Failure: stack modelling function (@test_stack_modelling.R#8)
4. Error: stacking function (@test_stacking.R#6)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.4
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘shinyFiles’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [39s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(SSDM)
Welcome to the SSDM package, you can launch the graphical user interface by typing gui() in the console.
>
> test_check("SSDM")
── 1. Error: ensemble function (@test_ensemble.R#7) ───────────────────────────
subscript out of bounds
1: modelling("SVM", Occurrences, Env, Xcol = "LONGITUDE", Ycol = "LATITUDE", select.thresh = 0,
verbose = FALSE) at testthat/test_ensemble.R:7
2: project(model, Env, ...)
3: project(model, Env, ...)
4: suppressWarnings(raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
}))
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
6: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
7: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
8: .local(object, ...)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 2. Error: ensemble modelling function (@test_ensemble_modelling.R#5) ───────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "MARS"), Occurrences, Env, rep = 1, Xcol = "LONGITUDE",
Ycol = "LATITUDE", ensemble.thresh = c(0), verbose = FALSE) at testthat/test_ensemble_modelling.R:5
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
── 3. Failure: stack modelling function (@test_stack_modelling.R#8) ───────────
`SSDM` inherits from `NULL` not `Stacked.SDM`.
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 4. Error: stacking function (@test_stacking.R#6) ───────────────────────────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "SVM"), Occ1, Env, rep = 1, Xcol = "LONGITUDE", Ycol = "LATITUDE",
name = "elliptica", ensemble.thresh = 0, verbose = FALSE) at testthat/test_stacking.R:6
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(name = "elliptica", thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 43 SKIPPED: 0 WARNINGS: 15 FAILED: 4
1. Error: ensemble function (@test_ensemble.R#7)
2. Error: ensemble modelling function (@test_ensemble_modelling.R#5)
3. Failure: stack modelling function (@test_stack_modelling.R#8)
4. Error: stacking function (@test_stacking.R#6)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘GUI.Rmd’ using rmarkdown
--- finished re-building ‘GUI.Rmd’
--- re-building ‘SSDM.Rmd’ using rmarkdown
Quitting from lines 92-96 (SSDM.Rmd)
Error: processing vignette 'SSDM.Rmd' failed with diagnostics:
unable to find an inherited method for function 'ensemble' for signature '"missing"'
--- failed re-building ‘SSDM.Rmd’
SUMMARY: processing the following file failed:
‘SSDM.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [42s/106s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(SSDM)
Welcome to the SSDM package, you can launch the graphical user interface by typing gui() in the console.
>
> test_check("SSDM")
── 1. Error: ensemble function (@test_ensemble.R#7) ───────────────────────────
subscript out of bounds
1: modelling("SVM", Occurrences, Env, Xcol = "LONGITUDE", Ycol = "LATITUDE", select.thresh = 0,
verbose = FALSE) at testthat/test_ensemble.R:7
2: project(model, Env, ...)
3: project(model, Env, ...)
4: suppressWarnings(raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
}))
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
6: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
7: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
8: .local(object, ...)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 2. Error: ensemble modelling function (@test_ensemble_modelling.R#5) ───────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "MARS"), Occurrences, Env, rep = 1, Xcol = "LONGITUDE",
Ycol = "LATITUDE", ensemble.thresh = c(0), verbose = FALSE) at testthat/test_ensemble_modelling.R:5
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
── 3. Failure: stack modelling function (@test_stack_modelling.R#8) ───────────
`SSDM` inherits from `NULL` not `Stacked.SDM`.
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 4. Error: stacking function (@test_stacking.R#6) ───────────────────────────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "SVM"), Occ1, Env, rep = 1, Xcol = "LONGITUDE", Ycol = "LATITUDE",
name = "elliptica", ensemble.thresh = 0, verbose = FALSE) at testthat/test_stacking.R:6
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(name = "elliptica", thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 43 SKIPPED: 0 WARNINGS: 15 FAILED: 4
1. Error: ensemble function (@test_ensemble.R#7)
2. Error: ensemble modelling function (@test_ensemble_modelling.R#5)
3. Failure: stack modelling function (@test_stack_modelling.R#8)
4. Error: stacking function (@test_stacking.R#6)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [43s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(SSDM)
Welcome to the SSDM package, you can launch the graphical user interface by typing gui() in the console.
>
> test_check("SSDM")
-- 1. Error: ensemble function (@test_ensemble.R#7) ---------------------------
subscript out of bounds
1: modelling("SVM", Occurrences, Env, Xcol = "LONGITUDE", Ycol = "LATITUDE", select.thresh = 0,
verbose = FALSE) at testthat/test_ensemble.R:7
2: project(model, Env, ...)
3: project(model, Env, ...)
4: suppressWarnings(raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
}))
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
6: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
7: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
8: .local(object, ...)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
-- 2. Error: ensemble modelling function (@test_ensemble_modelling.R#5) -------
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "MARS"), Occurrences, Env, rep = 1, Xcol = "LONGITUDE",
Ycol = "LATITUDE", ensemble.thresh = c(0), verbose = FALSE) at testthat/test_ensemble_modelling.R:5
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
-- 3. Failure: stack modelling function (@test_stack_modelling.R#8) -----------
`SSDM` inherits from `NULL` not `Stacked.SDM`.
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
-- 4. Error: stacking function (@test_stacking.R#6) ---------------------------
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "SVM"), Occ1, Env, rep = 1, Xcol = "LONGITUDE", Ycol = "LATITUDE",
name = "elliptica", ensemble.thresh = 0, verbose = FALSE) at testthat/test_stacking.R:6
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(name = "elliptica", thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
== testthat results ===========================================================
OK: 43 SKIPPED: 0 WARNINGS: 15 FAILED: 4
1. Error: ensemble function (@test_ensemble.R#7)
2. Error: ensemble modelling function (@test_ensemble_modelling.R#5)
3. Failure: stack modelling function (@test_stack_modelling.R#8)
4. Error: stacking function (@test_stacking.R#6)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [35s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(SSDM)
Welcome to the SSDM package, you can launch the graphical user interface by typing gui() in the console.
>
> test_check("SSDM")
── 1. Error: ensemble function (@test_ensemble.R#7) ───────────────────────────
subscript out of bounds
1: modelling("SVM", Occurrences, Env, Xcol = "LONGITUDE", Ycol = "LATITUDE", select.thresh = 0,
verbose = FALSE) at testthat/test_ensemble.R:7
2: project(model, Env, ...)
3: project(model, Env, ...)
4: suppressWarnings(raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
}))
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
6: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
7: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
8: .local(object, ...)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 2. Error: ensemble modelling function (@test_ensemble_modelling.R#5) ───────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "MARS"), Occurrences, Env, rep = 1, Xcol = "LONGITUDE",
Ycol = "LATITUDE", ensemble.thresh = c(0), verbose = FALSE) at testthat/test_ensemble_modelling.R:5
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
── 3. Failure: stack modelling function (@test_stack_modelling.R#8) ───────────
`SSDM` inherits from `NULL` not `Stacked.SDM`.
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 4. Error: stacking function (@test_stacking.R#6) ───────────────────────────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "SVM"), Occ1, Env, rep = 1, Xcol = "LONGITUDE", Ycol = "LATITUDE",
name = "elliptica", ensemble.thresh = 0, verbose = FALSE) at testthat/test_stacking.R:6
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(name = "elliptica", thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 43 SKIPPED: 0 WARNINGS: 15 FAILED: 4
1. Error: ensemble function (@test_ensemble.R#7)
2. Error: ensemble modelling function (@test_ensemble_modelling.R#5)
3. Failure: stack modelling function (@test_stack_modelling.R#8)
4. Error: stacking function (@test_stacking.R#6)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [47s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(SSDM)
Welcome to the SSDM package, you can launch the graphical user interface by typing gui() in the console.
>
> test_check("SSDM")
── 1. Error: ensemble function (@test_ensemble.R#7) ───────────────────────────
subscript out of bounds
1: modelling("SVM", Occurrences, Env, Xcol = "LONGITUDE", Ycol = "LATITUDE", select.thresh = 0,
verbose = FALSE) at testthat/test_ensemble.R:7
2: project(model, Env, ...)
3: project(model, Env, ...)
4: suppressWarnings(raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
}))
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
6: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
7: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
8: .local(object, ...)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 2. Error: ensemble modelling function (@test_ensemble_modelling.R#5) ───────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "MARS"), Occurrences, Env, rep = 1, Xcol = "LONGITUDE",
Ycol = "LATITUDE", ensemble.thresh = c(0), verbose = FALSE) at testthat/test_ensemble_modelling.R:5
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
── 3. Failure: stack modelling function (@test_stack_modelling.R#8) ───────────
`SSDM` inherits from `NULL` not `Stacked.SDM`.
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 4. Error: stacking function (@test_stacking.R#6) ───────────────────────────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "SVM"), Occ1, Env, rep = 1, Xcol = "LONGITUDE", Ycol = "LATITUDE",
name = "elliptica", ensemble.thresh = 0, verbose = FALSE) at testthat/test_stacking.R:6
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(name = "elliptica", thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 43 SKIPPED: 0 WARNINGS: 15 FAILED: 4
1. Error: ensemble function (@test_ensemble.R#7)
2. Error: ensemble modelling function (@test_ensemble_modelling.R#5)
3. Failure: stack modelling function (@test_stack_modelling.R#8)
4. Error: stacking function (@test_stacking.R#6)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘GUI.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘GUI.Rmd’
--- re-building ‘SSDM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-96 (SSDM.Rmd)
Error: processing vignette 'SSDM.Rmd' failed with diagnostics:
unable to find an inherited method for function 'ensemble' for signature '"missing"'
--- failed re-building ‘SSDM.Rmd’
SUMMARY: processing the following file failed:
‘SSDM.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [36s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(SSDM)
Welcome to the SSDM package, you can launch the graphical user interface by typing gui() in the console.
>
> test_check("SSDM")
── 1. Error: ensemble function (@test_ensemble.R#7) ───────────────────────────
subscript out of bounds
1: modelling("SVM", Occurrences, Env, Xcol = "LONGITUDE", Ycol = "LATITUDE", select.thresh = 0,
verbose = FALSE) at testthat/test_ensemble.R:7
2: project(model, Env, ...)
3: project(model, Env, ...)
4: suppressWarnings(raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
}))
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
6: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
7: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
8: .local(object, ...)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 2. Error: ensemble modelling function (@test_ensemble_modelling.R#5) ───────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "MARS"), Occurrences, Env, rep = 1, Xcol = "LONGITUDE",
Ycol = "LATITUDE", ensemble.thresh = c(0), verbose = FALSE) at testthat/test_ensemble_modelling.R:5
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
── 3. Failure: stack modelling function (@test_stack_modelling.R#8) ───────────
`SSDM` inherits from `NULL` not `Stacked.SDM`.
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
── 4. Error: stacking function (@test_stacking.R#6) ───────────────────────────
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "SVM"), Occ1, Env, rep = 1, Xcol = "LONGITUDE", Ycol = "LATITUDE",
name = "elliptica", ensemble.thresh = 0, verbose = FALSE) at testthat/test_stacking.R:6
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(name = "elliptica", thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 43 SKIPPED: 0 WARNINGS: 15 FAILED: 4
1. Error: ensemble function (@test_ensemble.R#7)
2. Error: ensemble modelling function (@test_ensemble_modelling.R#5)
3. Failure: stack modelling function (@test_stack_modelling.R#8)
4. Error: stacking function (@test_stacking.R#6)
Error: testthat unit tests failed
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.4
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-release-windows-ix86+x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(SSDM)
Welcome to the SSDM package, you can launch the graphical user interface by typing gui() in the console.
>
> test_check("SSDM")
-- 1. Error: ensemble function (@test_ensemble.R#7) ---------------------------
subscript out of bounds
1: modelling("SVM", Occurrences, Env, Xcol = "LONGITUDE", Ycol = "LATITUDE", select.thresh = 0,
verbose = FALSE) at testthat/test_ensemble.R:7
2: project(model, Env, ...)
3: project(model, Env, ...)
4: suppressWarnings(raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
}))
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
6: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
7: raster::predict(Env, model, fun = function(model, x) {
x = as.data.frame(x)
for (i in seq_len(length(Env@layers))) {
if (Env[[i]]@data@isfactor) {
x[, i] = as.factor(x[, i])
x[, i] = droplevels(x[, i])
levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
}
}
return(predict(model, x))
})
8: .local(object, ...)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
-- 2. Error: ensemble modelling function (@test_ensemble_modelling.R#5) -------
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "MARS"), Occurrences, Env, rep = 1, Xcol = "LONGITUDE",
Ycol = "LATITUDE", ensemble.thresh = c(0), verbose = FALSE) at testthat/test_ensemble_modelling.R:5
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'ensemble' for signature '"missing"'
-- 3. Failure: stack modelling function (@test_stack_modelling.R#8) -----------
`SSDM` inherits from `NULL` not `Stacked.SDM`.
Error in factors[[j]] : subscript out of bounds
Error in factors[[j]] : subscript out of bounds
-- 4. Error: stacking function (@test_stacking.R#6) ---------------------------
unable to find an inherited method for function 'ensemble' for signature '"missing"'
1: ensemble_modelling(c("CTA", "SVM"), Occ1, Env, rep = 1, Xcol = "LONGITUDE", Ycol = "LATITUDE",
name = "elliptica", ensemble.thresh = 0, verbose = FALSE) at testthat/test_stacking.R:6
2: do.call(ensemble, algo)
3: (new("nonstandardGenericFunction", .Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"),
ensemble.thresh = c(0.75), weight = TRUE, thresh = 1001, uncertainty = TRUE,
verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)))(name = "elliptica", thresh = 1001, uncertainty = TRUE, ensemble.metric = "AUC",
ensemble.thresh = 0, weight = TRUE, verbose = FALSE)
4: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list(structure("missing", package = "methods")), new("nonstandardGenericFunction",
.Data = function (x, ..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
{
return(standardGeneric("ensemble"))
}, generic = structure("ensemble", package = "SSDM"), package = "SSDM", group = list(),
valueClass = character(0), signature = c("x", "name", "ensemble.metric", "ensemble.thresh",
"weight", "thresh", "uncertainty", "verbose", "GUI"), default = NULL, skeleton = (function (x,
..., name = NULL, ensemble.metric = c("AUC"), ensemble.thresh = c(0.75),
weight = TRUE, thresh = 1001, uncertainty = TRUE, verbose = TRUE, GUI = FALSE)
stop("invalid call in method dispatch to 'ensemble' (no default method)", domain = NA))(x,
..., name = name, ensemble.metric = ensemble.metric, ensemble.thresh = ensemble.thresh,
weight = weight, thresh = thresh, uncertainty = uncertainty, verbose = verbose,
GUI = GUI)), <environment>)
5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
== testthat results ===========================================================
OK: 43 SKIPPED: 0 WARNINGS: 15 FAILED: 4
1. Error: ensemble function (@test_ensemble.R#7)
2. Error: ensemble modelling function (@test_ensemble_modelling.R#5)
3. Failure: stack modelling function (@test_stack_modelling.R#8)
4. Error: stacking function (@test_stacking.R#6)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Quitting from lines 92-96 (SSDM.Rmd)
Error: processing vignette 'SSDM.Rmd' failed with diagnostics:
unable to find an inherited method for function 'ensemble' for signature '"missing"'
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64