[ Started: 2023-05-31 00:08:09 CEST ]
[ decoupleR v2.5.0 for BioC-3.17 from https://github.com/saezlab/decoupleR@master ]

* using log directory ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2023-05-31_0003/decoupleR/decoupleR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.5.0’
* 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  8.8Mb
  sub-directories of 1Mb or more:
    doc       6.5Mb
    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
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-31 00:08:33] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Contains 3 files.
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-31 00:08:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-31 00:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-31 00:08:33] [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_dorothea
> ### Title: DoRothEA gene regulatory network.
> ### Aliases: get_dorothea
> 
> ### ** Examples
> 
> dorothea <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))
[2023-05-31 00:10:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-31 00:10:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-31 00:10:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`

 *** caught segfault ***
address 0x7f53dbe2c548, 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)})(3L, col_types = list(cols = list(dorothea_level = 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=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&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())     {        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)    }, col_types = list(cols = list(dorothea_level = list()),         default = list(), delim = NULL), progress = FALSE, show_col_types = FALSE)
11: do.call(omnipath_download, download_args)
12: import_omnipath(query_type = "interactions", resources = resources,     organism = organism, dorothea_levels = dorothea_levels, datasets = "dorothea",     fields = fields, default_fields = default_fields, references_by_resource = references_by_resource,     exclude = exclude, strict_evidences = strict_evidences, ...)
13: OmnipathR::dorothea(organism = organism, dorothea_levels = c("A",     "B", "C", "D"), genesymbols = T)
14: dplyr::select(., "source_genesymbol", "target_genesymbol", "is_stimulation",     "is_inhibition", "consensus_direction", "consensus_stimulation",     "consensus_inhibition", "dorothea_level")
15: dplyr::distinct(., .data$source_genesymbol, .data$dorothea_level,     .data$target_genesymbol, .keep_all = TRUE)
16: dplyr::mutate(., dorothea_level = unlist(map(.data$dorothea_level,     function(lvl) {        stringr::str_split(lvl, ";")[[1]][[1]]    })))
17: mutate(., mor = ifelse(.data$is_stimulation & .data$is_inhibition,     ifelse(.data$consensus_stimulation, 1, -1), ifelse(.data$is_stimulation,         1, ifelse(.data$is_inhibition, -1, 1))))
18: mutate(., mor = .data$mor/unlist(map(.data$dorothea_level, function(lvl) {    weight_dict[[lvl]]})))
19: dplyr::select(., "source_genesymbol", "dorothea_level", "target_genesymbol",     "mor")
20: OmnipathR::dorothea(organism = organism, dorothea_levels = c("A",     "B", "C", "D"), genesymbols = T) %>% dplyr::select("source_genesymbol",     "target_genesymbol", "is_stimulation", "is_inhibition", "consensus_direction",     "consensus_stimulation", "consensus_inhibition", "dorothea_level") %>%     dplyr::distinct(.data$source_genesymbol, .data$dorothea_level,         .data$target_genesymbol, .keep_all = TRUE) %>% dplyr::mutate(dorothea_level = unlist(map(.data$dorothea_level,     function(lvl) {        stringr::str_split(lvl, ";")[[1]][[1]]    }))) %>% mutate(mor = ifelse(.data$is_stimulation & .data$is_inhibition,     ifelse(.data$consensus_stimulation, 1, -1), ifelse(.data$is_stimulation,         1, ifelse(.data$is_inhibition, -1, 1)))) %>% mutate(mor = .data$mor/unlist(map(.data$dorothea_level,     function(lvl) {        weight_dict[[lvl]]    }))) %>% dplyr::select("source_genesymbol", "dorothea_level",     "target_genesymbol", "mor")
21: get_dorothea(organism = "human", levels = c("A", "B", "C"))
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  44: test_code(NULL, exprs, env)
  45: source_file(path, env(env), wrap = wrap)
  46: FUN(X[[i]], ...)
  47: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  48: doTryCatch(return(expr), name, parentenv, handler)
  49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  50: tryCatchList(expr, classes, parentenv, handlers)
  51: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  52: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, wrap = wrap))
  53: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package)
  54: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package, parallel = parallel)
  55: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  56: test_check("decoupleR")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2023-05-31_0003/decoupleR/decoupleR.Rcheck/00check.log’
for details.

[ Finished: 2023-05-31 00:15:43 CEST ]