##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘OmnipathR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 ...Warning: program compiled against libxml 212 using older 211
 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:31] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 09:36:31] [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).
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:31] [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).
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:32] [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).
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:32] [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).
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] Cache locked: FALSE

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 09:36:44] [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).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [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).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [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).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [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).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 09:37:01] [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).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [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).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [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).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [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).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: all_uniprots
> ### Title: A table with all UniProt records
> ### Aliases: all_uniprots
> 
> ### ** Examples
> 
> human_swissprot_entries <- all_uniprots(fields = 'id')
[2025-01-22 09:37:43] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:43] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:43] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-22 09:37:43] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 09:40:46] [WARN]    [OmnipathR] HTTP 404
[2025-01-22 09:40:46] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2025-01-22 09:40:51] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 09:43:53] [WARN]    [OmnipathR] HTTP 404
[2025-01-22 09:43:53] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2025-01-22 09:43:58] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 09:47:00] [WARN]    [OmnipathR] HTTP 404
[2025-01-22 09:47:00] [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:
! HTTP 404
Backtrace:
     ▆
  1. ├─OmnipathR::all_uniprots(fields = "id")
  2. │ └─organism %<>% ncbi_taxid
  3. ├─OmnipathR::ncbi_taxid(.)
  4. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
  5. ├─purrr::map_int(., taxon_name, "ncbi")
  6. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
  7. │   ├─purrr:::with_indexed_errors(...)
  8. │   │ └─base::withCallingHandlers(...)
  9. │   ├─purrr:::call_with_cleanup(...)
 10. │   └─OmnipathR (local) .f(.x[[i]], ...)
 11. │     ├─... %>% if_null_len0(NA)
 12. │     └─OmnipathR::get_db("organisms")
 13. │       └─OmnipathR::load_db(key, param = param)
 14. │         ├─rlang::exec(loader, !!!param)
 15. │         └─OmnipathR (local) `<fn>`()
 16. │           ├─... %>% ...
 17. │           └─OmnipathR::ensembl_organisms()
 18. │             ├─... %>% ...
 19. │             └─OmnipathR::ensembl_organisms_raw()
 20. │               └─... %>% html_table()
 21. ├─OmnipathR:::if_null_len0(., NA)
 22. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 23. ├─OmnipathR:::is_empty_2(.)
 24. │ └─value %>% ...
 25. ├─dplyr::first(.)
 26. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 27. │   └─vctrs::vec_size(x)
 28. ├─dplyr::pull(., name_type)
 29. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 30. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 31. ├─dplyr::mutate(...)
 32. ├─dplyr::full_join(...)
 33. ├─dplyr::mutate(...)
 34. ├─dplyr::select(...)
 35. ├─rvest::html_table(.)
 36. ├─rvest::html_element(., "table")
 37. ├─xml2::read_html(.)
 38. ├─OmnipathR:::download_to_cache(., req_headers = user_agent())
 39. │ └─OmnipathR:::download_base(...)
 40. │   └─base::stop(result)
 41. └─purrr (local) `<fn>`(`<smplErrr>`)
 42.   └─cli::cli_abort(...)
 43.     └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Caused by error in `map_int()`:
  ℹ In index: 1.
  Caused by error:
  ! HTTP 404
  Class:   purrr_error_indexed/rlang_error/error/condition
  ── Error ('test_import.R:182:13'): (code run outside of `test_that()`) ─────────
  Error in `eval(code, test_env)`: object 'response' not found
  Backtrace:
      ▆
   1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:182:13
   2. └─tidyr::separate_rows(., sources, sep = ";")
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  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: 2 ERRORs, 5 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.