[ Started: 2022-11-20 01:11:55 CET ] [ decoupleR v2.3.2 for BioC-3.16 from https://github.com/saezlab/decoupleR@master ] * using log directory ‘/home/omnipath/testing/decoupler/bioc-3.16/2022-11-20_0109/decoupleR/decoupleR.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘decoupleR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘decoupleR’ version ‘2.3.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘decoupleR’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: doc 5.6Mb extdata 1.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE [2022-11-20 01:12:16] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-11-20 01:12:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-11-20 01:12:16] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2022-11-20 01:12:16] [TRACE] [OmnipathR] Contains 3 files. [2022-11-20 01:12:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2022-11-20 01:12:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-11-20 01:12:16] [TRACE] [OmnipathR] Pandoc version: `2.5`. [2022-11-20 01:12:17] [TRACE] [OmnipathR] Cache locked: FALSE * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘decoupleR-Ex.R’ failed The error most likely occurred in: > ### Name: get_progeny > ### Title: Pathway RespOnsive GENes for activity inference (PROGENy). > ### Aliases: get_progeny > > ### ** Examples > > progeny <- get_progeny(organism='human', top=500) [2022-11-20 01:12:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2022-11-20 01:12:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2022-11-20 01:12:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` *** caught segfault *** address 0x7fddc020a6a4, cause 'invalid permissions' 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)})(3L, 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/annotations?resources=PROGENy&license=academic", fun = function (Segmentation fault (core dumped) * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: *** caught segfault *** address 0x7fc474023668, cause 'invalid permissions' 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/annotations?resources=PROGENy&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_colSegmentation fault (core dumped) * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘decoupleR.Rmd’ using ‘UTF-8’... OK ‘pw_bk.Rmd’ using ‘UTF-8’... OK ‘pw_sc.Rmd’ using ‘UTF-8’... OK ‘tf_bk.Rmd’ using ‘UTF-8’... OK ‘tf_sc.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘decoupleR.Rmd’ using rmarkdown Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union --- finished re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2022-11-20 01:13:35] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-11-20 01:13:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-11-20 01:13:35] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2022-11-20 01:13:35] [TRACE] [OmnipathR] Contains 2 files. [2022-11-20 01:13:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2022-11-20 01:13:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-11-20 01:13:35] [TRACE] [OmnipathR] Pandoc version: `2.5`. [2022-11-20 01:13:35] [TRACE] [OmnipathR] Cache locked: FALSE [2022-11-20 01:13:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2022-11-20 01:13:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2022-11-20 01:13:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` *** caught segfault *** address 0x7ff09e6b3893, 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, shoSegmentation fault (core dumped) * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 2 NOTEs See ‘/home/omnipath/testing/decoupler/bioc-3.16/2022-11-20_0109/decoupleR/decoupleR.Rcheck/00check.log’ for details. [ Finished: 2022-11-20 01:13:38 CET ]