CRAN Package Check Results for Package mptools

Last updated on 2020-02-15 01:01:31 CET.

Check Details

Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘intro.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.
    Extracting simulation results from file:
    /home/ripley/R/Lib32/mptools/example.mp
    Extracting population metadata from file:
    /home/ripley/R/Lib32/mptools/example.mp
    Extracting simulation results from file:
    /home/ripley/R/Lib32/mptools/example.mp
    rgdal: version: 1.4-8, (SVN revision 845)
     Geospatial Data Abstraction Library extensions to R successfully loaded
     Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
     Path to GDAL shared files: /usr/local/share/gdal
     GDAL binary built with GEOS: TRUE
     Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
     Path to PROJ.4 shared files: (autodetected)
     Linking to sp version: 1.3-2
    Extracting simulation results from file:
    /home/ripley/R/Lib32/mptools/example.mp
    Creating gif animation.
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: magick_image_write(image, format, quality, depth, density, comment)
     2: magick::image_write(anim, path = output)
     3: magick.convert(files = files, output = output, loop = loop, interval = interval, dispose = dispose)
     4: animation::im.convert(ff, output = outfile, extra.opts = "-dispose Background", clean = TRUE)
     5: mp_animate(spdf, habitat = stack(tifs), outfile = "dynamics.gif", zlim = c(0, 800), width = 630, height = 615, overwrite = TRUE)
     6: eval(expr, envir, enclos)
     7: eval(expr, envir, enclos)
     8: withVisible(eval(expr, envir, enclos))
     9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    13: evaluate::evaluate(...)
    14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    15: 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$render, options)))
    16: block_exec(params)
    17: call_block(x)
    18: process_group.block(group)
    19: process_group(group)
    20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    21: process_file(text, output)
    22: knit(input, text = text, envir = envir, quiet = quiet)
    23: knit2html(..., force_v1 = TRUE)
    24: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    25: vweave(...)
    26: engine$weave(file, quiet = quiet, encoding = enc)
    27: doTryCatch(return(expr), name, parentenv, handler)
    28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    29: tryCatchList(expr, classes, parentenv, handlers)
    30: tryCatch({ engine$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)))})
    31: tools:::buildVignettes(dir = "/home/ripley/R/packages/tests32/mptools.Rcheck/vign_test/mptools", ser_elibs = "/tmp/Rtmp9Ka4Nh/filef3f62a1695b.rds")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86