[ Started: 2024-04-07 18:44:01 CEST ] [ liana v0.1.13 for BioC-3.19 from https://github.com/saezlab/liana@master (4c323df 2023-11-03 14:35:54) ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘liana’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘liana_cc2tensor.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 '' [2024-04-07 18:44:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-07 18:44:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 18:44:36] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-07 18:44:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-07 18:44:36] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-07 18:44:36] [TRACE] [OmnipathR] Contains 1 files. [2024-04-07 18:44:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-07 18:44:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-07 18:44:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 18:44:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-07 18:44:36] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-07 18:44:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-07 18:44:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 18:44:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-07 18:44:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 18:44:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-07 18:44:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 18:44:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-07 18:44:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 18:44:36] [TRACE] [OmnipathR] Cache locked: FALSE 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 = FALSE, prompt = FALSE, comment = "##", highlight = TRUE, size = "normalsize", background = "#F7F7F7", strip.white = TRUE, cache = 0, cache.path = "liana_cc2tensor_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/RtmpU2fkDc/Rbuild801c068272873/liana/vignettes/liana_cc2tensor_files/figure-html/", dev = "svg", dev.args = NULL, dpi = 192, fig.ext = "svg", fig.width = 16, fig.height = 12, 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 = FALSE, error = FALSE, message = FALSE, render = NULL, ref.label = NULL, child = NULL, engine = "R", split = FALSE, include = TRUE, purl = TRUE, crop = TRUE, label = "unnamed-chunk-4", code = c("# Plot", "sce %>%", " get_abundance_summary(sample_col = \"context\",", " idents_col = \"cell\", ", " min_cells = 10, # min cells per sample", " min_samples = 3, # min samples", " min_prop = 0.2 # min prop of samples", " ) %>%", " plot_abundance_summary()", "", "# filter non abundant celltypes", "sce <- liana::filter_nonabundant_celltypes(sce,", " sample_col = \"context\",", " idents_col = \"cell\")" ), out.width.px = "100%", out.height.px = 1152, params.src = "message=FALSE, warning=FALSE, fig.width=16, fig.height=12", fig.alt = NULL, fig.num = 1), envir = , 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: 2024-04-07 18:44:52 CEST ]