[ Started: 2023-06-21 18:39:08 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
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:16] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Contains 1 files.
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:16] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-06-21 18:39:17] [INFO]    [wppi] Executing WPPI workflow.
[2023-06-21 18:39:17] [INFO]    [wppi] Collecting database knowledge.
[2023-06-21 18:39:17] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-06-21 18:39:17] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-06-21 18:39:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-06-21 18:39:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-21 18:39:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-21 18:39:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:17] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2023-06-21 18:39:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-06-21 18:39:17] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-06-21 18:39:17] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-06-21 18:39:20] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:20] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2023-06-21 18:39:20] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 293469 records
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2023-06-21 18:39:20] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-06-21 18:39:20] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2023-06-21 18:39:20] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2023-06-21 18:39:20] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`

 *** caught segfault ***
address 0x7f931a6424f2, 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, lazy = should_read_lazy()) {    tokenizer <- tokenizer_tsv(na = na, quoted_na = quoted_na,         quote = quote, comment = comment, trim_ws = trim_ws,         skip_empty_rows = skip_empty_rows)    if (edition_first()) {        return(read_delimited(file, tokenizer, col_names = col_names,             col_types = col_types, locale = locale, skip = skip,             skip_empty_rows = skip_empty_rows, comment = comment,             n_max = n_max, guess_max = guess_max, progress = progress,             show_col_types = show_col_types))    }    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 = lazySegmentation fault (core dumped)
[ Finished: 2023-06-21 18:39:21 CEST ]