[ Started: 2023-08-10 22:34:51 CEST ]
[ dorothea v1.7.3 for BioC-3.17 from https://github.com/saezlab/dorothea@master ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘dorothea’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dorothea.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2023-08-10 22:35:27] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-08-10 22:35:27] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Contains 1 files.
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-08-10 22:35:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-08-10 22:35:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-08-10 22:35:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-08-10 22:35:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-08-10 22:35:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-08-10 22:35:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-08-10 22:35:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-08-10 22:35:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-08-10 22:35:31] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2023-08-10 22:35:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-08-10 22:35:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-08-10 22:35:33] [INFO]    [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2023-08-10 22:35:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-08-10 22:35:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-08-10 22:35:33] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2023-08-10 22:35:33] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2023-08-10 22:35:46] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2023-08-10 22:35:59] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2023-08-10 22:39:35] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
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, options, envir) {    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 = "dorothea_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/RtmpPt9oav/Rbuild229f232272b6e1/dorothea/vignettes/dorothea_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 = "n_genes", code = c("n_genes <- net %>%",     "  group_by(source) %>%", "  summarize(n = n())", "", "ggplot(data=n_genes, aes(x=n)) +",     "  geom_density() +", "  theme(text = element_text(size=12)) +",     "  xlab('Number of target genes') +", "  ylab('densities') +",     "  theme_bw() +", "  theme(legend.position = \"none\")",     ""), out.width.px = "100%", out.height.px = 480, params.src = "n_genes",     fig.alt = NULL, fig.num = 1), envir = <environment>)
 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.block(group)
13: process_group(group)
14: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0") &&         !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e))
15: withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0") &&         !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e)),     error = function(e) {        setwd(wd)        write_utf8(res, output %n% stdout())        message("\nQuitting from lines ", paste(current_lines(i),             collapse = "-"), if (labels[i] != "")             sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile")))    })
16: process_file(text, output)
17: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
18: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
19: vweave_rmarkdown(...)
20: engine$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: 2023-08-10 22:39:43 CEST ]