[ Started: 2024-04-29 17:35:57 CEST ]
[ progeny v1.17.3 for BioC-3.19 from https://github.com/saezlab/progeny@master (cad6be0 2023-01-30 11:01:10) ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘progeny’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘progeny.Rmd’ using rmarkdown
Warning: package ‘BiocStyle’ was built under R version 4.5.0
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering.
For better results use image_read_svg() which uses the rsvg package.

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: magick_image_write(image, format, quality, depth, density, comment,     compression)
 2: magick::image_write(magick::image_trim(img), x)
 3: plot_crop(f)
 4: in_dir(d, expr)
 5: in_base_dir(for (f in get_plot_files()) plot_crop(f))
 6: (function (before, ...) {    if (before)         return()    in_base_dir(for (f in get_plot_files()) plot_crop(f))})(before = FALSE, options = list(eval = TRUE, echo = TRUE, results = "markup",     tidy = FALSE, tidy.opts = NULL, collapse = TRUE, prompt = FALSE,     comment = "#>", highlight = TRUE, size = "normalsize", background = "#F7F7F7",     strip.white = FALSE, cache = 0, cache.path = "progeny_cache/html/",     cache.vars = NULL, cache.lazy = TRUE, dependson = NULL, autodep = FALSE,     cache.rebuild = FALSE, fig.keep = "high", fig.show = "asis",     fig.align = "default", fig.path = "/tmp/RtmpP0tC5u/Rbuild3ad2621fabd9b/progeny/vignettes/progeny_files/figure-html/",     dev = "svg", dev.args = NULL, dpi = 192, fig.ext = "svg",     fig.width = 8, fig.height = 5, fig.env = "figure", fig.cap = NULL,     fig.scap = NA, fig.lp = "fig:", fig.subcap = NULL, fig.pos = "",     out.width = "100%", out.height = NULL, out.extra = NULL,     fig.retina = 2, external = TRUE, sanitize = FALSE, interval = 1,     aniopts = "controls,loop", warning = TRUE, error = FALSE,     message = TRUE, render = NULL, ref.label = NULL, child = NULL,     engine = "R", split = FALSE, include = TRUE, purl = TRUE,     crop = TRUE, label = "w_dist", code = c("# Get top 100 significant genes per pathway",     "model_100 <- model %>%", "  group_by(pathway) %>%", "  slice_min(order_by = p.value, n = 200)",     "", "# Plot", "ggplot(data=model_100, aes(x=weight, color=pathway, fill=pathway)) +",     "  geom_density() +", "  theme(text = element_text(size=12)) +",     "  facet_wrap(~ pathway, scales='free') +", "  xlab('scores') +",     "  ylab('densities') +", "  theme_bw() +", "  theme(legend.position = \"none\")",     ""), out.width.px = "100%", out.height.px = 480, params.src = "w_dist",     fig.alt = NULL, fig.num = 1), envir = <environment>, name = "crop")
 7: do.call(hook, args, envir = envir)
 8: run_hooks(before = FALSE, options, env)
 9: eng_r(options)
10: block_exec(params)
11: call_block(x)
12: process_group(group)
13: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
14: withCallingHandlers(expr, error = function(e) {    loc = if (is.function(fun))         trimws(fun(label))    else ""    if (loc != "")         loc = sprintf(" at lines %s", loc)    message(one_string(handler(e, loc)))})
15: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(e, loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
16: process_file(text, output)
17: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
18: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
19: vweave_rmarkdown(...)
20: engine$weave(file, quiet = quiet, encoding = enc)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch({    engine$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)))})
25: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
[ Finished: 2024-04-29 17:36:06 CEST ]