[ Started: 2024-10-03 17:07:39 CEST ]
[ wppi v1.12.0 for BioC-3.19 from https://git.bioconductor.org/packages/wppi@RELEASE_3_19 (1ad2e46 2024-04-30 11:33:03) ]

* using log directory ‘/mnt/disk0/build/bioc-check/wppi/bioc-3.19/2024-10-03_1706/wppi/wppi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04 LTS
* using session charset: UTF-8
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.12.0’
* 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 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 ‘wppi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Licence 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
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:01] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-03 17:08:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:01] [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
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:09] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-03 17:08:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-03 17:08:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-03 17:08:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:10] [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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘wppi-Ex.R’ failed
The error most likely occurred in:

> ### Name: common_neighbors
> ### Title: Shared neighbors of connected vertices
> ### Aliases: common_neighbors
> 
> ### ** Examples
> 
> graph_op <- graph_from_op(wppi_omnipath_data())
[2024-10-03 17:08:23] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-03 17:08:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:23] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-10-03 17:08:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:23] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-10-03 17:08:23] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-10-03 17:08:23] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-10-03 17:08:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] HTTP 200
[2024-10-03 17:08:24] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:24] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-03 17:08:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:24] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-03 17:08:24] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:08:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:08:26] [WARN]    [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: HTTP error 503.
[2024-10-03 17:08:31] [TRACE]   [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:08:33] [WARN]    [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 2/3); error: HTTP error 503.
[2024-10-03 17:08:38] [TRACE]   [OmnipathR] Attempt 3/3: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:08:39] [ERROR]   [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 3/3); error: HTTP error 503.
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `open.connection()`:
! HTTP error 503.
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:::if_null_len0(., NA)
 34. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 35. ├─OmnipathR:::is_empty_2(.)
 36. │ └─value %>% ...
 37. ├─dplyr::first(.)
 38. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 39. │   └─vctrs::vec_size(x)
 40. ├─dplyr::pull(., name_type)
 41. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 42. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 43. ├─dplyr::mutate(...)
 44. ├─dplyr::full_join(...)
 45. ├─dplyr:::full_join.data.frame(...)
 46. │ └─dplyr::auto_copy(x, y, copy = copy)
 47. │   ├─dplyr::same_src(x, y)
 48. │   └─dplyr:::same_src.data.frame(x, y)
 49. │     └─base::is.data.frame(y)
 50. ├─oma_organisms() %>% select(-genome_source, -oma_version)
 51. ├─dplyr::select(., -genome_source, -oma_version)
 52. ├─OmnipathR::oma_organisms()
 53. │ └─... %>% ...
 54. ├─dplyr::mutate(...)
 55. ├─OmnipathR:::generic_downloader(...)
 56. │ ├─... %>% omnipath_cache_save(url = url, post = post)
 57. │ ├─rlang::exec(...)
 58. │ └─OmnipathR (local) `<fn>`(...)
 59. │   └─base::stop(result)
 60. ├─OmnipathR::omnipath_cache_save(., url = url, post = post)
 61. │ └─base::saveRDS(data, target_path)
 62. └─purrr (local) `<fn>`(`<smplErrr>`)
 63.   └─cli::cli_abort(...)
 64.     └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:42] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Contains 2 files.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-10-03 17:08:42] [INFO]    [wppi] Executing WPPI workflow.
[2024-10-03 17:08:42] [INFO]    [wppi] Collecting database knowledge.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-10-03 17:08:42] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:42] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2024-10-03 17:08:42] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-10-03 17:08:42] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2024-10-03 17:08:44] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:44] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2024-10-03 17:08:44] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 312812 records
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2024-10-03 17:08:44] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:44] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2024-10-03 17:08:44] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-10-03 17:08:44] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-10-03 17:08:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2024-10-03 17:08:50] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2024-10-03 17:08:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2024-10-03 17:08:51] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 773774 records
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] HTTP 200
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-03 17:08:51] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:08:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:08:54] [WARN]    [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: HTTP error 503.
[2024-10-03 17:08:59] [TRACE]   [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:09:00] [WARN]    [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 2/3); error: HTTP error 503.
[2024-10-03 17:09:05] [TRACE]   [OmnipathR] Attempt 3/3: `https://omabrowser.org/All/oma-species.txt`
[2024-10-03 17:09:06] [ERROR]   [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 3/3); error: HTTP error 503.

Quitting from lines 80-102 [workflow] (wppi_workflow.Rmd)
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `open.connection()`:
! HTTP error 503.
--- failed re-building ‘wppi_workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘wppi_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/wppi/bioc-3.19/2024-10-03_1706/wppi/wppi.Rcheck/00check.log’
for details.

[ Finished: 2024-10-03 17:09:09 CEST ]