[ Started: 2023-07-03 23:39:46 CEST ]
[ dorothea v1.7.3 for BioC-3.16 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
[2023-07-03 23:40:23] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-03 23:40:23] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Contains 1 files.
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-03 23:40:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-03 23:40:23] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-07-03 23:40:23] [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`
[2023-07-03 23:40:23] [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`
[2023-07-03 23:40:23] [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 0x7f0993ff5183, 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, col_names = TRUE, col_types = NULL, col_select = NULL,     id = NULL, locale = default_locale(),Segmentation fault (core dumped)
[ Finished: 2023-07-03 23:40:26 CEST ]