[ Started: 2023-05-31 00:28:24 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 '' [2023-05-31 00:28:59] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2023-05-31 00:28:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-05-31 00:28:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-31 00:28:59] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-05-31 00:28:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-05-31 00:28:59] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-05-31 00:28:59] [TRACE] [OmnipathR] Contains 1 files. [2023-05-31 00:28:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-05-31 00:28:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-05-31 00:28:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-31 00:28:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-05-31 00:28:59] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-05-31 00:28:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-05-31 00:28:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-31 00:28:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-05-31 00:28:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-31 00:28:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-05-31 00:28:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-31 00:28:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-05-31 00:28:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-31 00:28:59] [TRACE] [OmnipathR] Cache locked: FALSE [2023-05-31 00:29:00] [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` [2023-05-31 00:29:00] [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` [2023-05-31 00:29:00] [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` *** caught segfault *** address 0x7ffac9e7662c, cause 'memory not mapped' Traceback: 1: vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, col_types = col_types, id = id, skip = skip, col_select = col_select, name_repair = .name_repair, na = na, quote = quote, trim_ws = trim_ws, escape_double = escape_double, escape_backslash = escape_backslash, comment = comment, skip_empty_rows = skip_empty_rows, locale = locale, guess_max = guess_max, n_max = n_max, altrep = vroom_altrep(altrep), num_threads = num_threads, progress = progress) 2: vroom::vroom(file, delim = "\t", col_names = col_names, col_types = col_types, col_select = { { col_select } }, id = id, .name_repair = name_repair, skip = skip, n_max = n_max, na = na, quote = quote, comment = comment, skip_empty_rows = skip_empty_rows, trim_ws = trim_ws, escape_double = TRUE, escape_backslash = FALSE, locale = locale, guess_max = guess_max, show_col_types = show_col_types, progress = progress, altrep = lazy, num_threads = num_threads) 3: (function (file, colSegmentation fault (core dumped) [ Finished: 2023-05-31 00:29:02 CEST ]