[ Started: 2022-10-18 20:46:45 CEST ]
[ OmnipathR v3.4.7 for BioC-3.15 from https://github.com/saezlab/OmnipathR@RELEASE_3_15 ]
* using log directory ‘/home/omnipath/testing/omnipathr/bioc-3.15/2022-10-18_2041/OmnipathR/OmnipathR.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 ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.4.7’
* 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 ‘OmnipathR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rmarkdown’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2022-10-18 20:47:06] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-10-18 20:47:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-10-18 20:47:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2022-10-18 20:47:06] [TRACE]   [OmnipathR] Pandoc version: `2.5`.
[2022-10-18 20:47:06] [TRACE]   [OmnipathR] Cache locked: FALSE
* 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: filter_intercell
> ### Title: Filter intercell annotations
> ### Aliases: filter_intercell
> 
> ### ** Examples
> 
> ic <- import_omnipath_intercell()
[2022-10-18 20:50:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2022-10-18 20:50:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2022-10-18 20:50:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`

 *** caught segfault ***
address 0x7f68a440c4c1, 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)})("https://omnipathdb.org/intercell?license=academic", col_types = list(    cols = list(), default = list(), delim = NULL), progress = FALSE,     show_col_types = FALSE)
 4: exec(fun, url, !!!args)
 5: download_base(url, fun, ...)
 6: (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/intercell?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, qSegmentation fault (core dumped)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK
  ‘db_manager.Rmd’ using ‘UTF-8’... OK
  ‘drug_targets.Rmd’ using ‘UTF-8’... OK
  ‘extra_attrs.Rmd’ using ‘UTF-8’... OK
  ‘nichenet.Rmd’ using ‘UTF-8’... OK
  ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK
  ‘paths.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/omnipath/testing/omnipathr/bioc-3.15/2022-10-18_2041/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2022-10-18 20:55:23 CEST ]