[ Started: 2023-07-04 18:37:24 CEST ]
[ wppi v1.6.0 for BioC-3.16 from https://github.com/AnaGalhoz37/wppi@main ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘wppi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-04 18:37:31] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Contains 1 files.
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-04 18:37:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-04 18:37:31] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-07-04 18:37:32] [INFO]    [wppi] Executing WPPI workflow.
[2023-07-04 18:37:32] [INFO]    [wppi] Collecting database knowledge.
[2023-07-04 18:37:32] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-07-04 18:37:32] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-07-04 18:37:32] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-07-04 18:37:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-07-04 18:37:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-04 18:37:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-07-04 18:37:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-07-04 18:37:32] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2023-07-04 18:37:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-07-04 18:37:32] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-07-04 18:37:32] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`

 *** caught segfault ***
address 0x7fc069efdf97, 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 = progreSegmentation fault (core dumped)
[ Finished: 2023-07-04 18:37:40 CEST ]