[ Started: 2023-06-21 18:37:52 CEST ] [ OmnipathR v3.6.6 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2023-06-21 18:38:01] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-06-21 18:38:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-06-21 18:38:01] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-06-21 18:38:01] [TRACE] [OmnipathR] Contains 1 files. [2023-06-21 18:38:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-06-21 18:38:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-06-21 18:38:01] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-06-21 18:38:01] [TRACE] [OmnipathR] Cache locked: FALSE [2023-06-21 18:38:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-06-21 18:38:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-06-21 18:38:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2023-06-21 18:38:02] [INFO] [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `unknown` to `started`. [2023-06-21 18:38:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`. [2023-06-21 18:38:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f4de1f63d60f35d18bb262dd6de84d1cccd9cc97-1.rds`. [2023-06-21 18:38:02] [INFO] [OmnipathR] Download ready [key=f4de1f63d60f35d18bb262dd6de84d1cccd9cc97, version=1] [2023-06-21 18:38:02] [INFO] [OmnipathR] Cache item `f4de1f63d60f35d18bb262dd6de84d1cccd9cc97` version 1: status changed from `started` to `ready`. [2023-06-21 18:38:04] [SUCCESS] [OmnipathR] Downloaded 71649 interactions. [2023-06-21 18:38:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-06-21 18:38:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-06-21 18:38:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-06-21 18:38:06] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2023-06-21 18:38:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2023-06-21 18:38:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2023-06-21 18:38:06] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2023-06-21 18:38:06] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2023-06-21 18:38:07] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships. [2023-06-21 18:38:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-06-21 18:38:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2023-06-21 18:38:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` *** caught segfault *** address 0x7fc21a9dd4cc, 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 = lazy, num_threads = num_threads)})(4L, col_types = list(cols = list(), default = list(), delim = NULL), progress = FALSE, show_col_types = FALSE) 4: exec(fun, the_url, !!!args) 5: doTryCatch(return(expr), name, parentenv, handler) 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 8: tryCatch(exec(fun, the_url, !!!args), error = identity) 9: download_base(url, fun, ...) 10: (function (url, fun, ...) { from_cache <- omnipath_cache_load(url = url) if (!is.null(from_cache)) { log_info("Loaded from cache: `%s`", url) return(from_cache) } result <- download_base(url, fun, ...) omnipath_cache_save(data = result, url = url) return(result)})(url = "https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic", fun = 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()) Segmentation fault (core dumped) [ Finished: 2023-06-21 18:38:09 CEST ]