CRAN Package Check Results for Package graphsim

Last updated on 2020-04-25 01:53:03 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.2 8.52 117.43 125.95 NOTE
r-devel-linux-x86_64-debian-gcc 0.1.2 8.29 85.17 93.46 OK
r-devel-linux-x86_64-fedora-clang 0.1.2 144.20 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1.2 139.64 NOTE
r-devel-windows-ix86+x86_64 0.1.2 23.00 136.00 159.00 OK
r-patched-linux-x86_64 0.1.2 9.39 108.46 117.85 OK
r-patched-osx-x86_64 0.1.2 NOTE
r-patched-solaris-x86 0.1.2 199.70 WARN
r-release-linux-x86_64 0.1.2 7.21 98.59 105.80 OK
r-release-windows-ix86+x86_64 0.1.2 18.00 97.00 115.00 OK
r-release-osx-x86_64 0.1.2 NOTE
r-oldrel-windows-ix86+x86_64 0.1.2 8.00 134.00 142.00 OK
r-oldrel-osx-x86_64 0.1.2 NOTE

Check Details

Version: 0.1.2
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'vdiffr'
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.2
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘utils’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘run_example_pathways.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 ‘run_example_pathways.Rmd’
    
    --- re-building ‘plots_directed.Rmd’ using knitr
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    --- finished re-building ‘plots_directed.Rmd’
    
    Segmentation Fault - core dumped
    --- re-building ‘plots_viral_quantitate.Rmd’ using knitr
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Output at: demo.gif
    
     *** 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: im.convert(img.files, output = path.expand(movie.name), convert = convert, cmd.fun = cmd.fun, clean = clean, extra.opts = extra.opts)
     5: saveGIF({ count = 0 for (i in 1:length(Glist)) { plot(Glist[[i]], layout = L, vertex.label = NA, vertex.size = 4, vertex.color = V(G)$color, vertex.frame.color = "white", edge.arrow.size = 1, edge.color = E(G)$color) count = count + 1 title(main = "Graph simulation example (200 nodes)", sub = paste("Time = ", count), cex.main = 1.2, cex.sub = 1) }}, interval = 1, movie.name = "demo2.gif", ani.width = 350, ani.height = 350)
     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: engine$weave(file, quiet = quiet, encoding = enc)
    26: doTryCatch(return(expr), name, parentenv, handler)
    27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    28: tryCatchList(expr, classes, parentenv, handlers)
    29: tryCatch({ engine$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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    30: tools:::.buildOneVignette("plots_viral_quantitate.Rmd", "/home/ripley/R/packages/tests32/graphsim.Rcheck/vign_test/graphsim", TRUE, FALSE, "plots_viral_quantitate", "UTF-8", "/tmp/Rtmpfta4CK/working_dir/RtmpDAaiV1/file6b79278b1b76.rds")
    An irrecoverable exception occurred. R is aborting now ...
    --- re-building ‘test_graph_convergent.Rmd’ using knitr
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    --- finished re-building ‘test_graph_convergent.Rmd’
    
    --- re-building ‘test_graph_divergent.Rmd’ using knitr
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    --- finished re-building ‘test_graph_divergent.Rmd’
    
    --- re-building ‘test_graph_network.Rmd’ using knitr
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    --- finished re-building ‘test_graph_network.Rmd’
    
    Profiling Timer Expired
    --- re-building ‘test_graph_network_inhibiting.Rmd’ using knitr
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    --- re-building ‘test_graph_reconvergent.Rmd’ using knitr
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    --- finished re-building ‘test_graph_reconvergent.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘plots_viral_quantitate.Rmd’ ‘test_graph_network_inhibiting.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86