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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.13.0’
* 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 whether startup messages can be suppressed ... NOTE
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:22] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 09:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:22] [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
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:56] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 09:39:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:39:56] [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())
[2024-05-30 09:40:48] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-30 09:40:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 09:40:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:40:48] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-30 09:40:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 09:40:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 09:40:48] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-30 09:40:48] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-30 09:40:48] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-30 09:40:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-30 09:40:55] [WARN]    [OmnipathR] HTTP 403
[2024-05-30 09:40:55] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-05-30 09:41:00] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-30 09:41:00] [WARN]    [OmnipathR] HTTP 403
[2024-05-30 09:41:00] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-05-30 09:41:05] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-30 09:41:05] [WARN]    [OmnipathR] HTTP 403
[2024-05-30 09:41:05] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 403
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. │ ├─rlang::exec(import_omnipath, !!!args)
 10. │ └─OmnipathR (local) `<fn>`(...)
 11. │   └─environment() %>% as.list %>% c(list(...)) %>% ...
 12. ├─OmnipathR:::omnipath_check_param(.)
 13. │ └─param$organisms %<>% map_int(ncbi_taxid)
 14. ├─purrr::map_int(., ncbi_taxid)
 15. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 16. │   ├─purrr:::with_indexed_errors(...)
 17. │   │ └─base::withCallingHandlers(...)
 18. │   ├─purrr:::call_with_cleanup(...)
 19. │   └─OmnipathR (local) .f(.x[[i]], ...)
 20. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 21. ├─purrr::map_int(., taxon_name, "ncbi")
 22. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 23. │   ├─purrr:::with_indexed_errors(...)
 24. │   │ └─base::withCallingHandlers(...)
 25. │   ├─purrr:::call_with_cleanup(...)
 26. │   └─OmnipathR (local) .f(.x[[i]], ...)
 27. │     ├─... %>% if_null_len0(NA)
 28. │     └─OmnipathR::get_db("organisms")
 29. │       └─OmnipathR::load_db(key, param = param)
 30. │         ├─rlang::exec(loader, !!!param)
 31. │         └─OmnipathR (local) `<fn>`()
 32. │           ├─... %>% ...
 33. │           └─OmnipathR::ensembl_organisms()
 34. │             ├─... %>% ...
 35. │             └─OmnipathR::ensembl_organisms_raw()
 36. │               └─... %>% html_table()
 37. ├─OmnipathR:::if_null_len0(., NA)
 38. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 39. ├─OmnipathR:::is_empty_2(.)
 40. │ └─value %>% ...
 41. ├─dplyr::first(.)
 42. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 43. │   └─vctrs::vec_size(x)
 44. ├─dplyr::pull(., name_type)
 45. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 46. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 47. ├─dplyr::mutate(...)
 48. ├─dplyr::full_join(...)
 49. ├─dplyr::mutate(...)
 50. ├─dplyr::select(...)
 51. ├─rvest::html_table(.)
 52. ├─rvest::html_element(., "table")
 53. ├─xml2::read_html(.)
 54. ├─OmnipathR:::download_to_cache(.)
 55. │ └─OmnipathR:::download_base(...)
 56. │   └─base::stop(result)
 57. └─purrr (local) `<fn>`(`<smplErrr>`)
 58.   └─cli::cli_abort(...)
 59.     └─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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck/00check.log’
for details.