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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (conda-forge gcc 14.2.0-1) 14.2.0
    GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.15.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wppi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... NOTE
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:35] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-07 10:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:35] [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
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:56] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-07 10:06:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-07 10:06:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-07 10:06:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-07 10:06:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:06:57] [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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘wppi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: common_neighbors
> ### Title: Shared neighbors of connected vertices
> ### Aliases: common_neighbors
> 
> ### ** Examples
> 
> graph_op <- graph_from_op(wppi_omnipath_data())
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2024-12-07 10:07:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2024-12-07 10:07:31] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-12-07 10:07:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-07 10:07:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:07:31] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-12-07 10:07:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-07 10:07:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 10:07:31] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-12-07 10:07:31] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-12-07 10:07:31] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-12-07 10:07:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-07 10:10:34] [WARN]    [OmnipathR] HTTP 404
[2024-12-07 10:10:34] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-12-07 10:10:39] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-07 10:13:40] [WARN]    [OmnipathR] HTTP 404
[2024-12-07 10:13:40] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-12-07 10:13:45] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-07 10:16:47] [WARN]    [OmnipathR] HTTP 404
[2024-12-07 10:16:47] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 404
Backtrace:
     ▆
  1. ├─wppi::graph_from_op(wppi_omnipath_data())
  2. │ └─op_data %>% ...
  3. ├─dplyr::select(., -c(source_genesymbol, target_genesymbol))
  4. ├─wppi::wppi_omnipath_data()
  5. │ └─... %>% select(seq(10))
  6. ├─dplyr::select(., seq(10))
  7. ├─rlang::exec(., !!!omnipath_param)
  8. ├─OmnipathR (local) `<fn>`(entity_type = "protein")
  9. │ └─OmnipathR::post_translational(...)
 10. │   ├─rlang::exec(omnipath_query, !!!args)
 11. │   └─OmnipathR (local) `<fn>`(...)
 12. │     └─environment() %>% as.list %>% c(list(...)) %>% ...
 13. ├─OmnipathR:::omnipath_check_param(.)
 14. │ └─param$organisms %<>% map_int(ncbi_taxid)
 15. ├─purrr::map_int(., ncbi_taxid)
 16. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 17. │   ├─purrr:::with_indexed_errors(...)
 18. │   │ └─base::withCallingHandlers(...)
 19. │   ├─purrr:::call_with_cleanup(...)
 20. │   └─OmnipathR (local) .f(.x[[i]], ...)
 21. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 22. ├─purrr::map_int(., taxon_name, "ncbi")
 23. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 24. │   ├─purrr:::with_indexed_errors(...)
 25. │   │ └─base::withCallingHandlers(...)
 26. │   ├─purrr:::call_with_cleanup(...)
 27. │   └─OmnipathR (local) .f(.x[[i]], ...)
 28. │     ├─... %>% if_null_len0(NA)
 29. │     └─OmnipathR::get_db("organisms")
 30. │       └─OmnipathR::load_db(key, param = param)
 31. │         ├─rlang::exec(loader, !!!param)
 32. │         └─OmnipathR (local) `<fn>`()
 33. │           ├─... %>% ...
 34. │           └─OmnipathR::ensembl_organisms()
 35. │             ├─... %>% ...
 36. │             └─OmnipathR::ensembl_organisms_raw()
 37. │               └─... %>% html_table()
 38. ├─OmnipathR:::if_null_len0(., NA)
 39. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 40. ├─OmnipathR:::is_empty_2(.)
 41. │ └─value %>% ...
 42. ├─dplyr::first(.)
 43. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 44. │   └─vctrs::vec_size(x)
 45. ├─dplyr::pull(., name_type)
 46. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 47. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 48. ├─dplyr::mutate(...)
 49. ├─dplyr::full_join(...)
 50. ├─dplyr::mutate(...)
 51. ├─dplyr::select(...)
 52. ├─rvest::html_table(.)
 53. ├─rvest::html_element(., "table")
 54. ├─xml2::read_html(.)
 55. ├─OmnipathR:::download_to_cache(., req_headers = user_agent())
 56. │ └─OmnipathR:::download_base(...)
 57. │   └─base::stop(result)
 58. └─purrr (local) `<fn>`(`<smplErrr>`)
 59.   └─cli::cli_abort(...)
 60.     └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00check.log’
for details.