CRAN Package Check Results for Package isocat

Last updated on 2019-12-07 08:49:29 CET.

Check Details

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