[ Started: 2023-05-31 01:29:24 CEST ]
[ OmnipathR v3.6.6 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.16/2023-05-31_0116/OmnipathR/OmnipathR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘3.6.6’
* 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   5.3Mb
* checking package 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2023-05-31 01:29:48] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-05-31 01:29:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-31 01:29:48] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-05-31 01:29:48] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-31 01:29:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-31 01:29:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-05-31 01:29:48] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-31 01:29:48] [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: evex_download
> ### Title: Interactions from the EVEX database
> ### Aliases: evex_download
> 
> ### ** Examples
> 
> evex_interactions <- evex_download()
[2023-05-31 01:34:07] [INFO]    [OmnipathR] Looking up in cache `http://evexdb.org/download/network-format/Metazoa/Homo_sapiens.tar.gz`: key=4bc028d7ec1a75171905c43a686770f3ddc78149, no version available.
[2023-05-31 01:34:07] [INFO]    [OmnipathR] Created new version for cache record 4bc028d7ec1a75171905c43a686770f3ddc78149: version 1.
[2023-05-31 01:34:07] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/4bc028d7ec1a75171905c43a686770f3ddc78149-1.tar.gz
[2023-05-31 01:34:07] [INFO]    [OmnipathR] Downloading `http://evexdb.org/download/network-format/Metazoa/Homo_sapiens.tar.gz`
[2023-05-31 01:34:07] [INFO]    [OmnipathR] Retrieving URL: `http://evexdb.org/download/network-format/Metazoa/Homo_sapiens.tar.gz`
[2023-05-31 01:34:07] [TRACE]   [OmnipathR] Attempt 1/3: `http://evexdb.org/download/network-format/Metazoa/Homo_sapiens.tar.gz`
[2023-05-31 01:34:08] [TRACE]   [OmnipathR] HTTP 200
[2023-05-31 01:34:08] [INFO]    [OmnipathR] Download ready [key=4bc028d7ec1a75171905c43a686770f3ddc78149, version=1]
[2023-05-31 01:34:08] [INFO]    [OmnipathR] Cache item `4bc028d7ec1a75171905c43a686770f3ddc78149` version 1: status changed from `unknown` to `ready`.
[2023-05-31 01:34:08] [TRACE]   [OmnipathR] Archive type `tar.gz`: `http://evexdb.org/download/network-format/Metazoa/Homo_sapiens.tar.gz`
[2023-05-31 01:34:08] [INFO]    [OmnipathR] Looking up in cache `http://evexdb.org/download/network-format/Metazoa/Homo_sapiens.tar.gz`: key=4bc028d7ec1a75171905c43a686770f3ddc78149, latest version=1.
[2023-05-31 01:34:08] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/4bc028d7ec1a75171905c43a686770f3ddc78149-1.tar.gz

 *** caught segfault ***
address 0x7fcb8ffd1593, 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(source_entrezgene_id = list(),     target_entrezgene_id = list()), default = list(), delim = NULL),     progress = FALSE)
 4: exec(., con, !!!reader_param)
 5: data %>% {    if (from_cache)         `attr<-`(., "origin", "cache")    else .}
 6: origin_cache(., archive_data$from_cache)
 7: data %>% `attr<-`("resource", resource) %>% `attr<-`("url", url) %>%     `attr<-`("source", source)
 8: source_attrs(., resource, archive_data$url)
 9: reader %>% exec(con, !!!reader_param) %>% origin_cache(archive_data$from_cache) %>%     source_attrs(resource, archive_data$url) %T>% {    if ("connection" %in% class(con))         base::close(con)}
10: archive_extractor(url_key = "evex", path = "EVEX_relations_9606.tab",     reader = read_tsv, reader_param = list(col_types = cols(source_entrezgene_id = col_character(),         target_entrezgene_id = col_character()), progress = FALSE),     resource = "EVEX")
11: evex_download()
An irrecoverable exception occurred. R is aborting now ...
Segmentation 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, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.16/2023-05-31_0116/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2023-05-31 01:46:03 CEST ]