[ Started: 2024-03-30 13:39:04 CET ] [ dorothea v1.7.4 for BioC-3.19 from https://github.com/saezlab/dorothea@master (1461fb7 2024-02-24 12:55:48) ] * 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 '' [2024-03-30 13:39:37] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-03-30 13:39:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Contains 1 files. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-30 13:39:38] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-30 13:39:38] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-30 13:39:38] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-30 13:39:38] [TRACE] [OmnipathR] HTTP 200 [2024-03-30 13:39:38] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-30 13:39:38] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-30 13:39:38] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-30 13:39:38] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-30 13:39:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-30 13:39:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-30 13:39:38] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-30 13:39:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:38] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-30 13:39:38] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-30 13:39:38] [TRACE] [OmnipathR] Looking up in cache: `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` [2024-03-30 13:39:38] [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` [2024-03-30 13:39:38] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.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` [2024-03-30 13:39:38] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.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` [2024-03-30 13:39:38] [TRACE] [OmnipathR] Attempting `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` [2024-03-30 13:39:38] [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` [2024-03-30 13:39:38] [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` [2024-03-30 13:39:42] [INFO] [OmnipathR] Successfully retrieved: `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` [2024-03-30 13:39:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:42] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`. [2024-03-30 13:39:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-03-30 13:39:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-03-30 13:39:44] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1] [2024-03-30 13:39:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-30 13:39:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-30 13:39:44] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`. [2024-03-30 13:39:44] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-03-30 13:39:56] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any [2024-03-30 13:40:09] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any [2024-03-30 13:43:37] [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/RtmpRxrB6p/Rbuild9ea3b29f5eb38/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 = ) 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")) rlang::entrace(e)) 15: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))}) 16: handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i])) 17: process_file(text, output) 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 20: vweave_rmarkdown(...) 21: engine$weave(file, quiet = quiet, encoding = enc) 22: doTryCatch(return(expr), name, parentenv, handler) 23: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 24: tryCatchList(expr, classes, parentenv, handlers) 25: 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)))}) 26: tools::buildVignettes(dir = ".", tangle = TRUE) An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped) [ Finished: 2024-03-30 13:43:45 CET ]