[ Started: 2023-06-24 18:33:18 CEST ]
[ decoupleR v2.5.2 for BioC-3.16 from https://github.com/saezlab/decoupleR@master ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘decoupleR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘decoupleR.Rmd’ using rmarkdown
--- finished re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2023-06-24 18:33:32] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:32] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Contains 1 files.
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:32] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:33] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:33] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:33] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-06-24 18:33:33] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] HTTP 200
[2023-06-24 18:33:33] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:33] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2023-06-24 18:33:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:33] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2023-06-24 18:33:33] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2023-06-24 18:33:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2023-06-24 18:33:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2023-06-24 18:33:34] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2023-06-24 18:33:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-24 18:33:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:34] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2023-06-24 18:33:34] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2023-06-24 18:33:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-06-24 18:33:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-24 18:33:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-06-24 18:33:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-06-24 18:33:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`

 *** caught segfault ***
address 0x7effdb7d99ad, 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(), na = c("", "NA"), quoted_na = TRUE,     quote = "\"", comment = "", trim_ws = TRUE, skip = 0, n_max = Inf,     guess_max = min(1000, n_max), progress = show_progress(),     name_repair = "unique", num_threads = readr_threads(), show_col_types = should_show_types(),     skip_empty_rows = TRUE, Segmentation fault (core dumped)
[ Finished: 2023-06-24 18:33:35 CEST ]