[ Started: 2023-03-21 18:02:33 CET ]
[ OmnipathR v3.7.5 for BioC-3.17 from https://github.com/saezlab/OmnipathR@master ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* 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 ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.7.5’
* 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  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
* 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 startup messages can be suppressed ... NOTE
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:51] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Contains 1 files.
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:51] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:57] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Contains 1 files.
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:02:57] [TRACE]   [OmnipathR] Cache locked: FALSE
build_index_impl: no visible binding for global variable ‘value’
complexes_search_index: no visible binding for global variable ‘name’
complexes_search_index: no visible binding for global variable ‘value’
complexes_search_index: no visible binding for global variable
  ‘resource’
enzsub_search_index: no visible binding for global variable
  ‘modification’
enzsub_search_index: no visible binding for global variable ‘resource’
interactions_search_index: no visible binding for global variable
  ‘attr_key’
interactions_search_index: no visible binding for global variable
  ‘value’
Undefined global functions or variables:
  attr_key modification name resource value
* 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 ... WARNING
Undocumented arguments in documentation object 'search_omnipath'
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: database_summary
> ### Title: Summary of the annotations and intercell database contents
> ### Aliases: database_summary
> 
> ### ** Examples
> 
> database_summary('annotations')
[2023-03-21 18:06:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations_summary?format=json`
[2023-03-21 18:06:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations_summary?format=json`
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations_summary?format=json`
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/annotations_summary?format=json` (encoding: UTF-8).
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:06:57] [INFO]    [OmnipathR] Cache item `029197d72b82eb9bdf11b278a40ff7e4d0be0165` version 1: status changed from `unknown` to `started`.
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/029197d72b82eb9bdf11b278a40ff7e4d0be0165-1.rds`.
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/029197d72b82eb9bdf11b278a40ff7e4d0be0165-1.rds`.
[2023-03-21 18:06:57] [INFO]    [OmnipathR] Download ready [key=029197d72b82eb9bdf11b278a40ff7e4d0be0165, version=1]
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-21 18:06:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-21 18:06:57] [INFO]    [OmnipathR] Cache item `029197d72b82eb9bdf11b278a40ff7e4d0be0165` version 1: status changed from `started` to `ready`.
Error in `vec_init()`:
! `x` must be a vector, not `NULL`.
Backtrace:
     ▆
  1. ├─OmnipathR::database_summary("annotations")
  2. │ └─... %>% if (return_df) tibble(.) %>% unnest_wider(1L) else .
  3. ├─purrr::map(...)
  4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
  6. ├─purrr::map(...)
  7. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  8. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
  9. ├─OmnipathR:::import_omnipath(., format = "json")
 10. │ └─result %<>% apply_exclude(exclude)
 11. ├─OmnipathR:::apply_exclude(., exclude)
 12. │ └─data %>% resources_colname
 13. ├─OmnipathR::resources_colname(.)
 14. │ └─... %>% first
 15. ├─dplyr::first(.)
 16. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 17. │   └─dplyr:::check_nth_default(default, x = x)
 18. │     └─vctrs::vec_init(x)
 19. └─vctrs:::stop_scalar_type(`<fn>`(NULL), "x", `<fn>`(vec_init()))
 20.   └─vctrs:::stop_vctrs(...)
 21.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
* 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, 1 WARNING, 3 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-21_1739/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2023-03-21 18:28:54 CET ]