Last updated on 2019-12-07 08:49:29 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 0.2.3 | 8.98 | 85.85 | 94.83 | ERROR | |
r-devel-linux-x86_64-debian-gcc | 0.2.3 | 7.77 | 80.20 | 87.97 | OK | |
r-devel-linux-x86_64-fedora-clang | 0.2.3 | 133.28 | NOTE | |||
r-devel-linux-x86_64-fedora-gcc | 0.2.3 | 134.64 | NOTE | |||
r-devel-windows-ix86+x86_64 | 0.2.3 | 16.00 | 149.00 | 165.00 | OK | |
r-devel-windows-ix86+x86_64-gcc8 | 0.2.3 | 14.00 | 110.00 | 124.00 | OK | |
r-patched-linux-x86_64 | 0.2.3 | 7.24 | 93.51 | 100.75 | OK | |
r-patched-solaris-x86 | 0.2.3 | 173.30 | NOTE | |||
r-release-linux-x86_64 | 0.2.3 | 7.37 | 93.35 | 100.72 | OK | |
r-release-windows-ix86+x86_64 | 0.2.3 | 16.00 | 106.00 | 122.00 | OK | |
r-release-osx-x86_64 | 0.2.3 | NOTE | ||||
r-oldrel-windows-ix86+x86_64 | 0.2.3 | 10.00 | 106.00 | 116.00 | OK | |
r-oldrel-osx-x86_64 | 0.2.3 | NOTE |
Version: 0.2.3
Check: examples
Result: ERROR
Running examples in 'isocat-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cumsumAtSamplingLocation
> ### Title: Cumulative sum at coordinates
> ### Aliases: cumsumAtSamplingLocation
>
> ### ** Examples
>
> # Generate example probability surface.
> myiso <- raster::rasterFromXYZ(isoscape)
> myiso_sd <- rasterFromXYZ(isoscape_sd)
> exampleSurface <- isotopeAssignmentModel(
+ ID = "A",
+ isotopeValue = -100,
+ SD_indv = 5,
+ precip_raster = myiso,
+ precip_SD_raster = myiso_sd,
+ nClusters = FALSE
+ )
> # Calculate odds ratio at specific point.
> set.seed(1)
> x <- sample( which( !is.na(exampleSurface[]) ), size = 1)
> pt <- raster::xyFromCell(exampleSurface, x)
> cumsumAtSamplingLocation(exampleSurface, Lat = pt[2], Lon = pt[1])
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
isocat
--- call from context ---
cumsumAtSamplingLocation(exampleSurface, Lat = pt[2], Lon = pt[1])
--- call from argument ---
if (class(p_atPoint) == "matrix") {
if (length(p_atPoint) != 1) {
stop("extracted value at coordinates must be of length one.")
}
else p_atPoint <- as.numeric(p_atPoint)
}
--- R stacktrace ---
where 1: cumsumAtSamplingLocation(exampleSurface, Lat = pt[2], Lon = pt[1])
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (indivraster, Lat, Lon)
{
if (!is.numeric(Lat) | !is.numeric(Lon))
stop("'Lat' and 'Lon' must both be numeric values.")
if (is.na(Lat) | is.na(Lon)) {
return(NA)
}
else {
indivcoords <- sp::SpatialPoints(cbind(Lon, Lat))
p_atPoint <- raster::extract(indivraster, indivcoords)
if (class(p_atPoint) == "matrix") {
if (length(p_atPoint) != 1) {
stop("extracted value at coordinates must be of length one.")
}
else p_atPoint <- as.numeric(p_atPoint)
}
vals <- stats::na.omit(indivraster[])
cumsumAtPoint <- vals[vals <= p_atPoint] %>% sum(na.rm = TRUE)
return(cumsumAtPoint)
}
}
<bytecode: 0x748dac0>
<environment: namespace:isocat>
--- function search by body ---
Function cumsumAtSamplingLocation in namespace isocat has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(p_atPoint) == "matrix") { :
the condition has length > 1
Calls: cumsumAtSamplingLocation
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.3
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'isocat.Rmd' using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
isocat
--- call from context ---
clusterSimmatrix(simmatrix = mySimilarityMatrix, dist_mthd = "correlation",
hclust_mthd = "average", nBoot = 1000, nClusters = FALSE,
r = seq(0.7, 1.4, by = 0.1))
--- call from argument ---
if (class(simmatrix) != "matrix") stop("Object 'x' is not of class 'Matrix'")
--- R stacktrace ---
where 1: clusterSimmatrix(simmatrix = mySimilarityMatrix, dist_mthd = "correlation",
hclust_mthd = "average", nBoot = 1000, nClusters = FALSE,
r = seq(0.7, 1.4, by = 0.1))
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,
encoding = encoding)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/isocat.Rcheck/vign_test/isocat",
ser_elibs = "/tmp/RtmpPpo3tx/file47a5343dd20f.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (simmatrix, dist_mthd = "correlation", hclust_mthd = "average",
nBoot = 1000, nClusters = FALSE, r = seq(0.7, 1.4, by = 0.1))
{
if (!requireNamespace("pvclust")) {
stop(" The \"pvclust\" package is required for parallel processing.")
}
if (class(simmatrix) != "matrix")
stop("Object 'x' is not of class 'Matrix'")
if (nClusters != FALSE) {
if (!is.numeric(nClusters))
stop("nClusters must be set to 'FALSE' or a numeric value.")
if (!requireNamespace("parallel")) {
stop(" The \"parallel\" package is required for parallel processing.")
}
if (!requireNamespace("doParallel")) {
stop(" The \"doParallel\" package is required for parallel processing.")
}
cl <- parallel::makeCluster(nClusters)
doParallel::registerDoParallel(cl)
}
else {
cl <- FALSE
}
suppressWarnings(result_ave <- pvclust::pvclust(data = data.matrix(simmatrix),
method.hclust = hclust_mthd, method.dist = dist_mthd,
nboot = nBoot, r = seq(0.7, 1.4, by = 0.1), parallel = cl))
if (nClusters != FALSE) {
parallel::stopCluster(cl)
}
return(result_ave)
}
<bytecode: 0x6146508>
<environment: namespace:isocat>
--- function search by body ---
Function clusterSimmatrix in namespace isocat has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 163-172 (isocat.Rmd)
Error: processing vignette 'isocat.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'isocat.Rmd'
SUMMARY: processing the following file failed:
'isocat.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.3
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘dplyr’
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