CRAN Package Check Results for Package MPTinR

Last updated on 2019-12-14 00:54:10 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.11.0 55.91 176.95 232.86 ERROR
r-devel-linux-x86_64-debian-gcc 1.11.0 40.81 137.84 178.65 ERROR
r-devel-linux-x86_64-fedora-clang 1.11.0 289.73 NOTE
r-devel-linux-x86_64-fedora-gcc 1.11.0 283.79 OK
r-devel-windows-ix86+x86_64 1.11.0 90.00 207.00 297.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.11.0 96.00 288.00 384.00 OK
r-patched-linux-x86_64 1.11.0 48.15 162.40 210.55 OK
r-patched-solaris-x86 1.11.0 295.30 OK
r-release-linux-x86_64 1.11.0 47.40 164.93 212.33 OK
r-release-windows-ix86+x86_64 1.11.0 84.00 206.00 290.00 OK
r-release-osx-x86_64 1.11.0 NOTE
r-oldrel-windows-ix86+x86_64 1.11.0 78.00 201.00 279.00 OK
r-oldrel-osx-x86_64 1.11.0 NOTE

Check Details

Version: 1.11.0
Check: examples
Result: ERROR
    Running examples in 'MPTinR-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: select.mpt
    > ### Title: Model Selection with MPTinR
    > ### Aliases: select.mpt
    >
    > ### ** Examples
    >
    >
    > # This example compares the three versions of the model in
    > # Riefer and Batchelder (1988, Figure 2)
    >
    > data(rb.fig2.data)
    > model2 <- system.file("extdata", "rb.fig2.model", package = "MPTinR")
    > model2r.r.eq <- system.file("extdata", "rb.fig2.r.equal", package = "MPTinR")
    > model2r.c.eq <- system.file("extdata", "rb.fig2.c.equal", package = "MPTinR")
    >
    > # The full (i.e., unconstrained) model
    > ref.model <- fit.mpt(rb.fig2.data, model2)
    Presenting the best result out of 5 minimization runs.
    [1] "Model fitting begins at 2019-12-12 19:34:47"
    [1] "Model fitting stopped at 2019-12-12 19:34:47"
    Time difference of 0.3366027 secs
    > # All r equal
    > r.equal <- fit.mpt(rb.fig2.data, model2, model2r.r.eq)
    Presenting the best result out of 5 minimization runs.
    [1] "Model fitting begins at 2019-12-12 19:34:47"
    [1] "Model fitting stopped at 2019-12-12 19:34:47"
    Time difference of 0.2303536 secs
    > # All c equal
    > c.equal <- fit.mpt(rb.fig2.data, model2, model2r.c.eq)
    Presenting the best result out of 5 minimization runs.
    [1] "Model fitting begins at 2019-12-12 19:34:47"
    [1] "Model fitting stopped at 2019-12-12 19:34:48"
    Time difference of 0.1773539 secs
    >
    > select.mpt(list(ref.model, r.equal, c.equal))
    Error in vapply(mpt.results, function(x) class(x[["data"]][["observed"]]), :
     values must be length 1,
     but FUN(X[[1]]) result is length 2
    Calls: select.mpt -> vapply
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.11.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'mptinr_introduction.Rnw' using knitr
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    MPTinR
     --- call from context ---
    prediction.plot(br.2htm.2, textConnection(mod_2htm_2), axis.labels = axis.labels,
     args.plot = list(main = "Absolute deviations (frequency scale)"))
     --- call from argument ---
    if (class(results[["data"]][["observed"]]) != "list") {
     data <- results[["data"]][["observed"]]
     exp <- results[["data"]][["predicted"]]
    } else {
     if (dataset == "aggregated") {
     data <- results[["data"]][["observed"]][["aggregated"]]
     exp <- results[["data"]][["predicted"]][["aggregated"]]
     }
     else {
     data <- results[["data"]][["observed"]][["individual"]][dataset,
     ]
     exp <- results[["data"]][["predicted"]][["individual"]][dataset,
     ]
     }
    }
     --- R stacktrace ---
    where 1: prediction.plot(br.2htm.2, textConnection(mod_2htm_2), axis.labels = axis.labels,
     args.plot = list(main = "Absolute deviations (frequency scale)"))
    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: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",
     file)) knit2pandoc else knit)(file, encoding = encoding,
     quiet = quiet, envir = globalenv(), ...)
    where 19: engine$weave(file, quiet = quiet, encoding = enc)
    where 20: doTryCatch(return(expr), name, parentenv, handler)
    where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 22: tryCatchList(expr, classes, parentenv, handlers)
    where 23: tryCatch({
     engine$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 24: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/MPTinR.Rcheck/vign_test/MPTinR",
     ser_elibs = "/tmp/Rtmp4UlCIE/file624c2f1e0205.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (results, model.filename, dataset = 1, absolute = TRUE,
     spacing = 2, axis.labels = NULL, ylim, model.type = c("easy",
     "eqn", "eqn2"), args.plot = list(), args.rect = list(),
     args.box = list(), args.points = list(), args.labels = list(),
     numbers = c("individual", "continuous"), pos.numbers = c("plot",
     "axis"), args.numbers = list(), args.abline = list(),
     abline)
    {
     tree <- .get.mpt.model(model.filename, model.type)
     categories.per.type <- vapply(tree, length, 0)
     n.trees <- length(categories.per.type)
     if (class(results[["data"]][["observed"]]) != "list") {
     data <- results[["data"]][["observed"]]
     exp <- results[["data"]][["predicted"]]
     }
     else {
     if (dataset == "aggregated") {
     data <- results[["data"]][["observed"]][["aggregated"]]
     exp <- results[["data"]][["predicted"]][["aggregated"]]
     }
     else {
     data <- results[["data"]][["observed"]][["individual"]][dataset,
     ]
     exp <- results[["data"]][["predicted"]][["individual"]][dataset,
     ]
     }
     }
     if (absolute)
     y.values <- data - exp
     else {
     y.values <- data
     y.values[data != 0] <- 2 * data[data != 0] * (log(data[data !=
     0]) - log(exp[data != 0]))
     }
     x.bool <- unlist(mapply(function(x, y, spacing) rep(c(y,
     FALSE), c(x, spacing)), categories.per.type, seq(categories.per.type),
     spacing = spacing, SIMPLIFY = FALSE))
     x.values <- which(x.bool != 0)
     xlim <- c(1, max(x.values))
     if (missing(ylim))
     ylim <- c(min(y.values), max(y.values))
     def.args.plot <- list(xlab = "", ylab = "", main = "")
     args.to.plot <- c(x = list(x.values), y = list(y.values),
     ylim = list(ylim), xaxt = "n", type = "n", args.plot,
     def.args.plot[!names(def.args.plot) %in% names(args.plot)])
     do.call("plot", args = args.to.plot)
     mean.trees <- vector("numeric", n.trees)
     def.args.rect <- list(col = "grey", border = "transparent",
     density = 30, angle = 45)
     args.to.rect <- c(args.rect, def.args.rect[!names(def.args.rect) %in%
     names(args.rect)])
     for (c in seq_along(categories.per.type)) {
     tmp.args.to.rect <- c(xleft = min(which(x.bool == c)) -
     1, ybottom = 1.5 * ylim[1], xright = max(which(x.bool ==
     c)) + 1, ytop = 1.5 * ylim[2], args.to.rect)
     do.call("rect", tmp.args.to.rect)
     mean.trees[c] <- mean(which(x.bool == c))
     }
     do.call("box", args.box)
     if (missing(abline))
     if (pos.numbers[1] == "axis")
     abline <- TRUE
     else abline <- FALSE
     def.args.abline <- list(col = "darkgrey")
     args.to.abline <- c(v = list(x.values), args.abline, def.args.abline[!names(def.args.abline) %in%
     names(args.abline)])
     if (abline)
     do.call("abline", args.to.abline)
     def.args.points <- list(pch = 1, cex = 2.25)
     args.to.points <- c(x = list(x.values), y = list(y.values),
     args.points, def.args.points[!names(def.args.points) %in%
     names(args.points)])
     do.call("points", args.to.points)
     def.args.axis <- list(line = -1)
     pos.numbers <- match.arg(pos.numbers, c("plot", "axis"),
     several.ok = TRUE)
     if (!is.null(numbers)) {
     numbers <- match.arg(numbers, c("individual", "continuous"),
     several.ok = TRUE)
     if (numbers[1] == "individual")
     numbers.pch <- unlist(lapply(rle(x.bool[x.bool !=
     0])[["lengths"]], seq_len))
     if (numbers[1] == "continuous")
     numbers.pch <- seq_along(y.values)
     if (pos.numbers[1] == "plot") {
     def.args.text <- list(labels = as.character(numbers.pch),
     cex = 0.7)
     args.to.text <- c(x = list(x.values), y = list(y.values),
     args.numbers, def.args.text[!names(def.args.text) %in%
     names(args.numbers)])
     do.call("text", args.to.text)
     }
     if (pos.numbers[1] == "axis") {
     def.args.axis2 <- list(labels = numbers.pch, cex.axis = 0.6,
     mgp = c(0, 0.3, 0))
     args.to.axis2 <- c(side = 1, at = list(x.values),
     args.numbers, def.args.axis2[!names(def.args.axis2) %in%
     names(args.numbers)])
     do.call("axis", args.to.axis2)
     def.args.axis <- list(line = 1)
     }
     }
     if (is.null(axis.labels))
     axis.labels <- paste("Tree", seq_len(n.trees))
     args.to.axis <- c(side = 1, at = list(mean.trees), labels = list(axis.labels),
     tick = FALSE, args.labels, def.args.axis[!names(def.args.axis) %in%
     names(args.labels)])
     do.call("axis", args.to.axis)
     invisible(list(x = x.values, y = y.values))
    }
    <bytecode: 0x8629098>
    <environment: namespace:MPTinR>
     --- function search by body ---
    Function prediction.plot in namespace MPTinR has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 593-600 (mptinr_introduction.Rnw)
    Error: processing vignette 'mptinr_introduction.Rnw' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'mptinr_introduction.Rnw'
    
    SUMMARY: processing the following file failed:
     'mptinr_introduction.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.11.0
Check: examples
Result: ERROR
    Running examples in ‘MPTinR-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: select.mpt
    > ### Title: Model Selection with MPTinR
    > ### Aliases: select.mpt
    >
    > ### ** Examples
    >
    >
    > # This example compares the three versions of the model in
    > # Riefer and Batchelder (1988, Figure 2)
    >
    > data(rb.fig2.data)
    > model2 <- system.file("extdata", "rb.fig2.model", package = "MPTinR")
    > model2r.r.eq <- system.file("extdata", "rb.fig2.r.equal", package = "MPTinR")
    > model2r.c.eq <- system.file("extdata", "rb.fig2.c.equal", package = "MPTinR")
    >
    > # The full (i.e., unconstrained) model
    > ref.model <- fit.mpt(rb.fig2.data, model2)
    Presenting the best result out of 5 minimization runs.
    [1] "Model fitting begins at 2019-12-13 18:03:17"
    [1] "Model fitting stopped at 2019-12-13 18:03:18"
    Time difference of 0.3108156 secs
    > # All r equal
    > r.equal <- fit.mpt(rb.fig2.data, model2, model2r.r.eq)
    Presenting the best result out of 5 minimization runs.
    [1] "Model fitting begins at 2019-12-13 18:03:18"
    [1] "Model fitting stopped at 2019-12-13 18:03:18"
    Time difference of 0.1726744 secs
    > # All c equal
    > c.equal <- fit.mpt(rb.fig2.data, model2, model2r.c.eq)
    Presenting the best result out of 5 minimization runs.
    [1] "Model fitting begins at 2019-12-13 18:03:18"
    [1] "Model fitting stopped at 2019-12-13 18:03:18"
    Time difference of 0.1828494 secs
    >
    > select.mpt(list(ref.model, r.equal, c.equal))
    Error in vapply(mpt.results, function(x) class(x[["data"]][["observed"]]), :
     values must be length 1,
     but FUN(X[[1]]) result is length 2
    Calls: select.mpt -> vapply
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.11.0
Check: installed package size
Result: NOTE
     installed size is 10.0Mb
     sub-directories of 1Mb or more:
     libs 9.0Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64